JP6877334B2 - Methods and Materials for Assessing Homologous Recombination Defects - Google Patents

Description

Related Applications This application is a US Provisional Application No. 62 / 037,764 filed on August 15, 2014, and a US Commonwealth Patent Application No. 14 / 507,412 filed on October 6, 2014 (“Application No. 412”). ”), All of which are incorporated herein by reference. This application, No. 412, was initially erroneously filed as a US common patent application and granted the above filing date. It is currently in the process of being converted to a US provisional application, for which no application number has yet been assigned. At the time the number was properly assigned by the United States Patent and Trademark Office, the International Application would further claim and be deemed to have claimed the priority benefit of the provisional application.

Background Cancer is a serious public health problem, with 562,340 people dying from cancer in the United States in 2009 alone. American Cancer Society, Cancer Facts & Figures 2009 (Non-Patent Document 1) (available on the American Cancer Society website). One of the most important challenges in cancer treatment is discovering the relevant clinically useful features of the patient's own cancer, followed by implementing the most appropriate treatment plan for the patient's cancer based on these features. It is to be. Although this field of personalized medicine is evolving, there is still a great need for better molecular diagnostic tools to characterize patient cancer.

American Cancer Society, Cancer Facts & Figures 2009

Summary This document evaluates samples (eg, cancer cells or nucleic acids derived from them) for homologous recombination defects (HRDs) (eg, HRD signatures) based on the detection of specific chromosomal abnormalities (“CA”). Regarding methods and materials. For example, this document provides methods and materials for detecting CA regions to determine if a cell (eg, a cancer cell) has an HRD (eg, exhibits an HRD signature). The document also provides materials and methods for identifying cancer patients who are likely to respond to a particular cancer treatment regimen based on the presence, absence, or severity of HRD. Throughout this document, HRD and homology-dependent repair (HDR) deficiency are used interchangeably, unless otherwise indicated.

Overall, one aspect of the invention features a method for assessing HRD in cancer cells or DNA derived from them (eg, genomic DNA). In some embodiments, the method comprises (a) in the sample or DNA derived from it, any human chromosome other than at least one pair of human chromosomes (eg, human X / Y sex chromosome pair) of the sample or DNA derived from it. Does it include a step of detecting a CA region in (pair) (as defined herein) and (b) a step of determining the number, size (eg, length), and / or characteristics of said CA region? , Or from these stages becomes essential. In some embodiments, the CA region is analyzed in several chromosomal pairs that represent the entire genome (eg, the number and size of CA regions are expected to represent the number and size of CA regions throughout the genome. Analyze enough chromosomes).

Various aspects of the invention involve the use of complex analysis of two or more types of CA regions to evaluate (eg, detect) HRD in a sample. The three CA regions useful in such methods include (1) a chromosomal region that exhibits heterozygosity (“LOH region” as defined herein) and (2) a telomere allelic imbalance. Chromosomal regions (“TAI regions” as defined herein), and (3) chromosomal regions that exhibit large transitions (“LST regions” as defined herein). CA regions with a particular size, chromosomal location or characteristics (eg, "indicator CA regions" as defined herein) are particularly useful in various aspects of the invention described herein.

Thus, in one aspect, the invention is a method of assessing (eg, detecting) HRD in a sample, (1) a LOH region (eg, herein) having a particular size or characteristic in the sample. Steps to determine the total number of "indicator LOH regions" defined therein; (2) TAI regions of a particular size or characteristic in a sample (eg, "indicator TAI regions" defined herein). ) Is provided; and (3) a method of assessing HRD in a sample based at least in part on the decisions made in (1) and (2). In another aspect, the invention is a method of assessing (eg, detecting) HRD in a sample, (1) a LOH region (eg, herein) having a particular size or characteristic in the sample. Steps to determine the total number of defined "indicator LOH regions"); (2) of LST regions of a particular size or characteristic in a sample (eg, "indicator LST regions" as defined herein). Provided are methods that include determining the total number; and assessing HRD in the sample, at least in part based on the determinations made in (3) (1) and (2). In another aspect, the invention is a method of assessing (eg, detecting) HRD in a sample, (1) a TAI region (eg, herein) having a particular size or characteristic in the sample. Steps to determine the total number of defined "indicator TAI regions"); (2) of LST regions of a particular size or characteristic in a sample (eg, "indicator LST regions" as defined herein). Provided are methods that include determining the total number; and assessing HRD in the sample, at least in part based on the determinations made in (3) (1) and (2). In another aspect, the invention is a method of assessing (eg, detecting) HRD in a sample, (1) a LOH region (eg, herein) having a particular size or characteristic in the sample. Steps to determine the total number of defined "indicator LOH regions"); (2) of TAI regions of a particular size or characteristic in a sample (eg, "indicator TAI regions" as defined herein). Steps to determine the total number; (3) Steps to determine the total number of LST regions of a particular size or characteristic in the sample (eg, "indicator LST regions" as defined herein); and (4). Provided are methods that include, at least in part, assessing (eg, detecting) HRD in a sample based on the decisions made in (1), (2) and (3).

In one aspect, the invention is a method of diagnosing the presence or absence of HRD in a patient sample, (1) a LOH region of a sample having a particular size or characteristic (eg, defined herein). The step of analyzing (eg, assaying) one or more patient samples to determine (eg, detect) the total number of "indicator LOH regions"); (2) a particular size of the sample. Alternatively, analyze one or more patient samples (eg, detect) to determine (eg, detect) the total number of characteristic TAI regions (eg, "indicator TAI regions" as defined herein). Stage (assay); and (3) Diagnose the presence of HRD in the patient sample if the number from (a) (1) and / or the number from (2) exceeds some reference number; or (3) ) (B) Provide a method comprising any of the steps of diagnosing the absence of HRD in a patient sample if neither the number from (1) nor the number from (2) exceeds any reference number. In another aspect, the invention is a method of diagnosing the presence or absence of HRD in a patient sample, (1) a LOH region of a sample having a particular size or characteristic (eg, defined herein). The step of analyzing (eg, assaying) one or more patient samples to determine (eg, detect) the total number of "indicator LOH regions"); (2) a particular size of the sample. Alternatively, analyze one or more patient samples (eg, detect) to determine (eg, detect) the total number of characteristic LST regions (eg, "indicator LST regions" as defined herein). Steps (assay); and (3) (a) Diagnose the presence of HRD in the patient sample if the number from (1) and / or the number from (2) exceeds some reference number; or ( 3) Provided is a method comprising any of the steps of diagnosing the absence of HRD in a patient sample if neither the number from (b) (1) nor the number from (2) exceeds any reference number. In another aspect, the invention is a method of diagnosing the presence or absence of HRD in a patient sample, (1) a TAI region of a sample having a particular size or characteristic (eg, defined herein). The step of analyzing (eg, assaying) one or more patient samples to determine (eg, detect) the total number of "indicator TAI regions"); (2) a particular size of the sample. Alternatively, analyze one or more patient samples (eg, detect) to determine (eg, detect) the total number of characteristic LST regions (eg, "indicator LST regions" as defined herein). Steps (assay); and (3) (a) Diagnose the presence of HRD in the patient sample if the number from (1) and / or the number from (2) exceeds some reference number; or ( 3) Provided is a method comprising any of the steps of diagnosing the absence of HRD in a patient sample if neither the number from (b) (1) nor the number from (2) exceeds any reference number. In another aspect, the invention is a method of diagnosing the presence or absence of HRD in a patient sample, (1) a LOH region of a sample having a particular size or characteristic (eg, defined herein). The step of analyzing (eg, assaying) one or more patient samples to determine (eg, detect) the total number of "indicator LOH regions"); (2) a particular size of the sample. Alternatively, analyze one or more patient samples (eg, detect) to determine (eg, detect) the total number of characteristic TAI regions (eg, "indicator TAI regions" as defined herein). Steps to assay; (3) To determine (eg, detect) the total number of LST regions with a particular size or characteristic (eg, "indicator LST region" as defined herein) in a sample. In addition to the steps of analyzing (eg, assaying) one or more patient samples; and (3) (a) numbers from (1), numbers from (2) and / or numbers from (3). At the stage of diagnosing the presence of HRD in the patient sample when the number of references exceeds any number; or when the number according to (3) (1), (2) or (3) does not exceed any number of references (b) Provided is a method comprising any of the steps of diagnosing the absence of HRD in a patient sample.

Various aspects of the invention involve using the average of three CA regions (eg, the arithmetic mean) to evaluate (eg, detect) HRD in a sample. The three CA regions useful in such methods include (1) a chromosomal region that exhibits heterozygosity (“LOH region” as defined herein) and (2) a telomere allelic imbalance. Includes chromosomal regions (“TAI regions” as defined herein) and (3) chromosomal regions that exhibit large-scale transitions (“LST regions” as defined herein). CA regions of a particular size or characteristic (eg, "indicator CA regions" as defined herein) may be particularly useful in various aspects of the invention described herein. Thus, in one aspect, the invention is a method of assessing (eg, detecting) HRD in a sample, (1) a LOH region (eg, herein) having a particular size or characteristic in the sample. Steps to determine the total number of "indicator LOH regions" defined therein; (2) TAI regions of a particular size or characteristic in a sample (eg, "indicator TAI regions" defined herein). ); (3) A step of determining the total number of LST regions having a specific size or characteristic (for example, "indicator LST region" as defined herein) in a sample; (4) ) To calculate the average of the decisions made in (1), (2) and (3) (eg, the arithmetic mean); and to the calculated average (eg, the arithmetic mean) obtained in (5) and (4). Provided are methods that include, at least in part, the step of assessing HRD in a sample.

In some embodiments, the HRD assessment (eg, detection) is derived from or calculated from the detected CA region (eg, representing or corresponding to it) score (as defined herein). Based on the "CA area score"). The score will be described in more detail below. In some embodiments, HRD is detected when the CA region score for the sample exceeds some threshold (eg, reference score or index CA region score), and optionally HRD is the CA region score for the sample (eg, reference score). Alternatively, the index CA region score, which in some embodiments may be the same threshold for positive detection), is not detected if it does not exceed any threshold. Those skilled in the art will identify in the opposite direction a score in the opposite direction (eg, if the CA region score is less than a certain threshold, but not if the score is above a certain threshold). You will easily understand what you can devise.

In some embodiments, the CA region score is defined as (1) the detected LOH region (“LOH region score” as defined herein), (2) the detected TAI region (defined herein). Derived or calculated from two or more of the detected LST regions (“LST region scores” as defined herein) and / or (3) detected LST regions (“TAI region scores”). A combination of scores to be (eg, representing or corresponding to it). In some embodiments, the LOH region score and the TAI region score are combined as follows to obtain the CA region score:
CA area score = A ^* (LOH area score) + B ^* (TAI area score)

In some embodiments, the LOH region score and the TAI region score are combined as follows to obtain the CA region score:
CA area score = 0.32 ^* (LOH area score) +0.68 ^* (TAI area score)

In some embodiments, the LOH region score and the LST region score are combined as follows to obtain the CA region score:
CA area score = A ^* (LOH area score) + B ^* (LST area score)

In some embodiments, the TAI region score and the LST region score are combined as follows to obtain the CA region score:
CA area score = A ^* (TAI area score) + B ^* (LST area score)

In some embodiments, the LOH region score, the TAI region score and the LST region score are combined as follows to obtain the CA region score:
CA area score = A ^* (LOH area score) + B ^* (TAI area score) + C ^* (LST area score)

In some embodiments, the LOH region score, the TAI region score and the LST region score are combined as follows to obtain the CA region score:
CA area score = 0.21 ^* (LOH area score) +0.67 ^* (TAI area score) +0.12 ^* (LST area score)

In some embodiments, the CA region score is defined as (1) the detected LOH region (“LOH region score” as defined herein), (2) the detected TAI region to obtain the CA region score. (“TAI region score” as defined herein) and / or (3) mean of detected LST regions (“LST region score” as defined herein) (eg, arithmetic mean). A combination of scores derived from or calculated from (eg, representing or corresponding to it):

In another aspect, the invention provides a method of predicting the status of the BRCA1 and BRCA2 genes in a sample. Such a method is similar to the method described above, but the determination of the CA region, LOH region, TAI region, LST region, or a score incorporating them assesses BRCA1 and / or BRCA2 deficiency in the sample ( For example, it is different in that it is used for detecting). In another aspect, the invention provides a method of predicting the response of a cancer patient to a cancer treatment regimen that includes a DNA damaging agent, anthracycline, topoisomerase I inhibitor, radiation, and / or PARP inhibitor. Such a method is similar to the method described above, but determining the CA, LOH, TAI, LST, or combined scores predicts that cancer patients are likely to respond to the cancer treatment regimen. The difference is that it is used to do this. In some embodiments, the patient is an untreated patient. In another aspect, the invention provides a method of treating cancer. Such methods are similar to those described above, but with specific treatment regimens based at least in part on determining the CA region, LOH region, TAI region, LST region, or a score that incorporates them. It differs in that it is given (recommended, prescribed, etc.). In another aspect, the invention treats cancer in a patient identified as having (or having) cancer cells determined to have the HRD (eg, HRD signature) described herein. It is characterized by the use of one or more drugs selected from the group consisting of DNA damaging agents, anthracyclines, topoisomerase I inhibitors and PARP inhibitors in the manufacture of drugs useful for the purpose. In another aspect, this document features a method for evaluating a sample for the presence of mutations in a gene derived from the HDR pathway. Such a method is similar to the method described above, but the determination of the CA region, LOH region, TAI region, LST region, or a score incorporating them is the presence of mutations in the gene derived from the HDR pathway ( Or absent) in that it is used to detect.

In another aspect, the invention provides a method for evaluating a patient. The method (a) determines whether a patient has (or has) cancer cells (or, for example, a CA region score greater than the reference CA region score) that exceeds the number of references in the CA region; and ( b) (1) If the patient is determined to have (or have) cancer cells that exceed the number of references in the CA region (or, for example, a CA region score that exceeds the reference CA region score), the patient is associated with HRD. The stage of diagnosing with cancer cells; or (b) (2) the patient does not (or has never) had more cancer cells than the number of references in the CA region (or, for example, the patient has a reference CA region score). Includes or includes the stage of diagnosing a patient as having no cancer cells with HRD if it is determined to have (or never had) cancer cells with a CA region score greater than From stage to essential.

In another aspect, the invention is useful for determining the total number or combined length of CA regions in at least one pair of chromosomes (or DNA derived from them) in a sample obtained from a cancer patient. , (A) Probability of HRD or HRD in the sample (eg, HRD signature), (b) Deficiency (or probability of deficiency) of the BRCA1 or BRCA2 gene in the sample, or (c) Cancer patients are DNA-damaging agents, anthra Hybrids with multiple polymorphic regions of human genomic DNA in the production of diagnostic kits that are also useful for detecting a high likelihood of responding to a cancer treatment regimen containing cyclins, topoisomerase I inhibitors, radiation, or PARP inhibitors. It is characterized by the use of multiple oligonucleotides that can be soybean.

In another aspect, the invention features a system for detecting HRD (eg, HRD signature) in a sample. The system is based on (a) a sample analyzer configured to generate multiple signals for genomic DNA of at least one pair of human chromosomes (or DNA derived from it) in a sample, and (b) multiple signals. Includes, or consists essentially of, a computer subsystem programmed to calculate the number or total length of CA regions in at least one pair of human chromosomes. The computer subsystem compares the number or total length of CA regions to the number of references and (a) the probability of HRD or HRD in the sample (eg, HRD signature), (b) the deletion of the BRCA1 or BRCA2 gene in the sample ( Or probable deficiency), or (c) programs to detect that cancer patients are more likely to respond to a cancer treatment regimen that includes DNA damage agents, anthracyclins, topoisomerase I inhibitors, radiation, or PARP inhibitors. can do. The system may include an output module configured to display (a), (b) or (c). The system may include an output module configured to display recommendations for the use of cancer treatment regimens.

In another aspect, the invention, when performed on a computer, is any CA region (the CA region is optionally an indicator) that resides on one or more human chromosomes other than the human X and Y sex chromosomes. A computer program product incorporated into a computer-readable medium to detect the presence or absence of a) CA region; and to give instructions to determine the total or total length of the CA region on one or more pairs of chromosomes. provide. The computer program product may contain other instructions.

In another aspect, the invention provides a diagnostic kit. The kit includes, or is essentially derived from, at least 500 oligonucleotides capable of hybridizing to multiple polymorphic regions of human genomic DNA (or DNA derived from it); and the computer program products provided herein. Become a target. Computer program products may be integrated into a computer-readable medium and, when run on a computer, any CA region that resides on one or more of human chromosomes other than the human X and Y sex chromosomes ( CA regions are optionally indicator CA regions) to detect the presence or absence; and give instructions to determine the total or total length of CA regions in one or more pairs of chromosomes. The computer program product may contain other instructions.

In any one or more aspects of the aspects of the invention described in the preceding paragraph, any one or more of the following may be applied as appropriate. The CA region can be determined on at least 2, 5, 10 or 21 pairs of human chromosomes. The cancer cells may be ovarian cancer cells, breast cancer cells, lung cancer cells or esophageal cancer cells. The number of references may be 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18 or 20, or more. Human chromosome 17 can be excluded from at least one pair of human chromosomes. The DNA damaging agent may be cisplatin, carboplatin, oxalaplatin, or picoplatin, the anthracycline may be epirubincin or doxorubicin, and the topoisomerase I inhibitor may be campothecin, topotecan or irinotecan. Or the PARP inhibitor may be iniparib, olaparib or velapirib. The patient may be an untreated patient.

Unless otherwise specified, all technical and scientific terms used herein have the same meaning as is generally understood by the trader in the art to which the present invention belongs. Methods and materials similar to or equivalent to those described herein can be used in the practice of the present invention, but suitable methods and materials are described below. All publications, patent applications, patents, and other references referred to herein are incorporated herein by reference in their entirety. In the event of inconsistency, this specification, including the definitions, will prevail. In addition, the materials, methods, and examples are merely exemplary and are not intended to be limiting.

Details of one or more aspects of the invention are shown in the following description and accompanying drawings. The materials, methods, and examples are merely exemplary and are not intended to be limiting. Other features, objectives, and advantages of the invention will be apparent from the description and drawings, as well as the claims.

A graph plotting allele dosages of breast cancer cells from freshly frozen samples from breast cancer patients, determined using SNP arrays (top) and high-throughput sequencing (bottom), along the length of the chromosome. Shown. The graph shows the allelic amount of breast cancer cells from the FFPE sample derived from the breast cancer patient plotted along the length direction of the chromosome, which was determined using the SNP array (top) and high-throughput sequencing (bottom). It is a flow chart of an exemplary process for evaluating the genome of a cell (eg, a cancer cell) for the HRD signature. FIG. 5 is a schematic representation of an example of a computer device and a mobile computer device that can be used to perform the techniques described herein. The LOH region scores by IHC subtype of breast cancer are shown. The top three panels are BRCA1 / 2 deficient samples. The bottom panel is a BRCA1 / 2 intact sample. The TAI region scores by IHC subtype of breast cancer are shown. The top three panels are BRCA1 / 2 deficient samples. The bottom panel is a BRCA1 / 2 intact sample. It shows the correlation between the LOH region score and the TAI region score. Correlation coefficient = 0.69. X-axis: LOH score; Y-axis: TAI score; Red dot: Intact sample; Blue dot ("X" is superimposed): BRCA1 / 2 deficient sample. The area under the dot is proportional to the number of samples with a combination of LOH score and TAI score. p = 10 ^-39 . The LOH region scores for the patients analyzed in Example 2 herein are shown. The top three panels are BRCA1 / 2 deficient samples. The bottom panel is a BRCA1 / 2 intact sample. The TAI region scores for the patients analyzed in Example 2 herein are shown. The top three panels are BRCA1 / 2 deficient samples. The bottom panel is a BRCA1 / 2 intact sample. The LST region scores for the patients analyzed in Example 2 herein are shown. The top three panels are BRCA1 / 2 deficient samples. The bottom panel is a BRCA1 / 2 intact sample. The comparison between LOH and TAI for the patients analyzed in Example 2 in the present specification is shown. X-axis: LOH score; Y-axis: TAI score; Red dot: Intact sample; Blue dot ("X" is superimposed): BRCA1 / 2 deficient sample. The area under the dot is proportional to the number of samples with a combination of LOH score and TAI score. The comparison between LOH and LST for the patients analyzed in Example 2 in the present specification is shown. X-axis: LOH score; Y-axis: LST score; Red dot: Intact sample; Blue dot ("X" is superimposed): BRCA1 / 2 deficient sample. The area under the dot is proportional to the number of samples with a combination of LOH score and LST score. The comparison between TAI and LST for the patients analyzed in Example 2 in the present specification is shown. X-axis: TAI score; Y-axis: LST score; Red dot: Intact sample; Blue dot ("X" is superimposed): BRCA1 / 2 deficient sample. The area under the dot is proportional to the number of samples with a combination of TAI score and LST score. For ovarian cancer cell samples with somatic BRCA mutations, germline BRCA mutations, low BRCA1 expression, or intact BRCA (normal BRCA), the number of LOH regions longer than 15 Mb and shorter than the entire chromosome was plotted. It is a graph. The size of the circle is proportional to the number of samples with such a number of LOH regions. All participants chart the HRD-LOH scores in BRCA 1/2 deficient (mutated or methylated) samples (upper panel) and intact samples (lower panel) in the breast cohort. All participants chart the HRD-TAI scores in BRCA1 / 2 deficient (mutated or methylated) samples (upper panel) and intact samples (lower panel) in the breast cohort. All participants chart the HRD-LST scores in BRCA1 / 2 deficient (mutated or methylated) samples (upper panel) and intact samples (lower panel) in the breast cohort. The average (eg, arithmetic mean) HRD-composite score (Y-axis) stratified by the Miller-Payne score (horizontal axis) in the cisplatin-1 and cisplatin-2 composite cohort is illustrated. It illustrates the Spearman correlation of three different scales of HR deficiency. The upper diagonal panel shows the correlation. The diagonal panel shows the density plot. It illustrates the association between clinical variables and HRD-composite scores. The association between clinical variables and BRCA1 / 2 deficiency is illustrated. Both the upper panel and the lower left panel show the proportion of BRCA1 / 2 deficient patients in each category of grade, stage and breast cancer type. The width of each bar is proportional to the number of patients in each category. The lower right panel shows conditional density estimates of age at diagnosis for BRCA1 / 2 deficiency. It illustrates the determination of high HRD with a reference score of 42 or higher. A histogram showing the distribution of HRD scores in the cisplatin cohort is shown. The four columns on the left represent low HRD, and the five columns on the right represent high HRD with a reference score above 42. The distribution of HRD scores in the pCR, RCB-I, RCB-II and RCB-III class reactions is illustrated. The box represents the interquartile range (IQR) of the score, and the horizontal line represents the median. The dotted line at position 42 represents the HRD threshold between the low and high scores. The reaction curve for the quantitative HRD score is shown. The curve is modeled by generalized logistic regression. The darkly painted boxes contrast and point to the probability of reaction in HR-deficient and non-deficient samples. The HRD scores for the individual HRD components (LOH, TAI, and LST) are illustrated.

Detailed Description Overall, one aspect of the invention features a method for assessing HRD in cancer cells or DNA derived from them (eg, genomic DNA). In some embodiments, the method determines, in (a) a sample or DNA derived from it, a CA region in at least one pair of human chromosomes or DNA derived from it; and (b) the number of said CA regions, Includes or consists essentially of steps to determine size (eg, length) and / or features.

As used herein, "chromosomal aberration" or "CA" means a somatic change in the chromosomal DNA of a cell that falls into at least one of three overlapping categories: LOH, TAI or LST. To do. Polymorphic loci in the human genome (eg, single nucleotide polymorphisms (SNPs)) are generally heterozygous in an individual's germline, which is typically one copy from the biological father. , To receive one copy from the biological mother. However, in somatic cells, this heterozygosity can change to homozygosity (via mutation). This change from heterozygosity to homozygosity is called heterozygous loss (LOH). LOH can occur by several mechanisms. For example, in some cases, a locus on one chromosome may be deleted in a somatic cell. Since the locus present in the genome of the affected cell has only one copy (rather than two copies), the locus still present on the other chromosome (or the other non-sex chromosome in the case of males) It becomes LOH. This type of LOH event results in a reduction in the number of copies. In other cases, the locus of one chromosome in the somatic cell (eg, one of the non-sex chromosomes in the case of male) is replaced by a copy of that locus from the other chromosome, thereby replacing. It may also eliminate any heterozygosity that may have been present within the locus. In such cases, the locus still present on each chromosome becomes the LOH locus, which can be referred to as the copy neutral LOH locus. Its use in determining LOH, and HRD, is described in detail in International Application No. PCT / US2011 / 040953 (published as WO / 2011/160063), all of which are herein by reference. Be incorporated.

A broader class of chromosomal abnormalities, including LOH, is an allelic imbalance. Allelic imbalance is when the relative number of copies (ie, the percentage of copies) at a particular locus in a somatic cell is different from that of a germline. For example, if the germline has 1 copy of allele A and 1 copy of allele B at a particular locus and the somatic cell has 2 copies of A and 1 copy of B, the percentage of copies in the somatic cell. Since (2: 1) is different from germline (1: 1), there is an allelic imbalance in its locus. LOH is an example of an allelic imbalance, as somatic cells have different proportions (1: 0 or 2: 0) of copies than germline (1: 1). However, an allergic imbalance is that more types of chromosomal abnormalities, such as 2: 1 in germline become 1: 1 in somatic cells; 1: 0 in germline becomes 1: 1 in somatic cells. Becoming 1; 1: 1 in germline becomes 2: 1 in somatic cells, etc. are also included in the range. Analysis of allelic imbalance regions in chromosomal telomeres is particularly useful in the present invention. Thus, a "telomere allelic imbalance region" or "TAI region" is defined as a region with an allelic imbalance that (a) extends toward one of the subtelomeres but (b) does not cross the centromere. Its use in the determination of TAI, and HRD, is described in detail in U.S. Patent Application Nos. 13 / 818,425 (published as US20130281312A1) and 14 / 466,208 (published as US20150038340A1), all of which are described in detail. Incorporated herein by reference.

A broader class of chromosomal abnormalities that still include LOH and TAI is referred to herein as a large transition (“LST”). LST refers to any somatic copy number transition (ie, discontinuity) that exists along the length of a chromosome, which is some maximum length (eg, 0.1, 0.2, 0.3, 0.4,). After sifting through areas shorter than 0.5, 0.6, 0.7, 0.8, 0.9, 1, 1.5, 2, 2.5, 3, 3.5, 4 megabases, or more, at least some minimum length (eg, at least 3, 4) , 5, 6, 7, 89, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or 20 megabases, or more). For example, after sifting off regions shorter than 3 megabases, somatic cells have a 1: 1 copy count, eg, over at least 10 megabases, followed by, for example, to at least 10 megabase regions with 2: 2 copies. If you have a discontinuity transition of, this is an LST. An alternative way to define the same phenomenon is as an LST region, which is at least some minimum length (eg, at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12). , 13, 14, 15, 16, 17, 18, 19 or 20 megabases), bordering it, and towards another region that also has at least this minimum length. Refers to a genomic region that has a discontinuity (ie, a transition) that changes. For example, after sifting off regions shorter than 3 megabases, somatic cells have at least 10 megabase regions with a 1: 1 copy count, at the border on one side, eg, 2: 2. If there is a discontinuity transition to a region of at least 10 megabases and there is a discontinuity transition to a region of at least 10 megabases with, for example, 1: 2 copies, on the other side boundary. Are two LSTs. This is because such copy number changes are not considered to be an allele imbalance (because the 1: 1 and 2: 2 copy ratios are the same, that is, there is no change in the copy ratio). Note that it is more extensive than imbalance. Its use in determining LST, and HRD, is described in detail in US Patent Application No. 14 / 402,254 (published as US20150140122A1), all of which is incorporated herein by reference.

Various cutoffs for LST scores can be used for "near diploid" and "near tetraploid" tumors to separate BRCA1 / 2 intact and BRCA1 / 2 deficient samples. The LST score can sometimes increase with ploidy in both intact and missing samples. As an alternative to using ploidy-specific cutoffs, in some embodiments, a modified LST score adjusted by ploidy: LSTm = LST-kP can be used, where P is ploidy in the equation. , K is a constant. Based on multivariate logistic regression analysis with defects as outcomes and LST and P as predictors, k = 15.5, provided that the best separation between intact and defective samples is a condition (but this). The vendor can also assume other values for k).

Chromosomal abnormalities can spread across a number of loci to define the extent of a region of chromosomal aberration referred to herein as the "CA region." Such a CA region may be of any length (eg, from a length less than about 1.5 Mb to a length equal to the overall length of the chromosome). The presence of many large CA regions (“indicator CA regions”) indicates a deficiency in the cell's homology-dependent repair (HDR) mechanism. For each type of CA (eg, LOH, TAI, LST), the definition of the CA domain, and therefore what constitutes the "indicator" domain, depends on the unique characteristics of the CA. For example, "LOH region" means any minimum number of contiguous loci exhibiting LOH, or any minimal sequence of genomic DNA having contiguous loci exhibiting LOH. The "TAI region", on the other hand, extends from the telomere to the rest of the chromosome, at least some minimum number of contiguous loci exhibiting an allergen imbalance (or from the telomere to the rest of the chromosome, allergen imbalance). Means any smallest sequence of genomic DNA with a contiguous locus that exhibits. LST has already been defined for regions of genomic DNA of at least some minimum size, so that "LST" and "LST regions" border on discontinuities or transitions from their copy count to another. It is used interchangeably herein to refer to the smallest number of consecutive loci (or any smallest sequence of genomic DNA) with the same number of copies.

In some embodiments, the CA region (either the LOH region, the TAI region, or the LST region) is at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14 , 15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90 or 100 megabases or longer, indicator CA region ( Either the indicator LOH area, the indicator TAI area, or the indicator LST area). In some embodiments, the indicator LOH region is approximately 1.5, 5, 12, 13, 14, 15, 16, 17 megabases or longer (preferably 14, 15, 16 megabases or longer, more preferably. Is a LOH region whose LOH region is shorter than the overall length of each chromosome in which it is located (15 megabases or longer). Alternatively or additionally, the total length of such indicator LOH region may be determined. In some embodiments, the indicator TAI region extends to (a) one of the suballeles, (b) does not cross the centromere, and (c) 1.5, 5, 12, 13, 14, 15, 16, 17 megabases or Longer (preferably 10, 11, 12 megabases or longer, more preferably 11 megabases or longer), TAI region with allelic imbalance. Alternatively or additionally, the total length of such indicator TAI regions may be determined. Since the concept of LST already includes some minimum size region, such minimum size is determined based on its ability to discriminate HRD from HDR intact samples, the indicator LST region used herein is Same as LST area. Moreover, the LST region score can be derived from either the number of regions showing LST or the number of LST discontinuities described above. In some embodiments, the minimum length of the stable copy count region bordering the LST discontinuity is at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14 , 15, 16, 17, 18, 19 or 20 megabases (preferably 8, 9, 10, 11 megabases or longer, more preferably 10 megabases), and the maximum area remaining unscreened is 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 1.5, 2, 2.5, 3, 3.5, 4 megabases or less (preferably 2, 2.5, 3, 3.5 or 4 megabases or it) Less than, more preferably less than 3 megabases).

As used herein, a sample is an indicator CA region (as described herein) or CA region score (as described herein) in which such a sample exceeds the number of references as described herein. If it has (as described herein), it has an "HRD signature", where a number or score above such a reference indicates a homologous recombination deficiency.

Thus, the invention as a whole involves detecting and quantifying the indicator CA region in a sample to determine if the cells in the sample (or the cells from which the DNA in the sample is derived) have the HRD signature. Often this is to compare the number of indicator CA regions (or test values or scores derived or calculated from it and corresponding to such numbers) to the number of references or indexes (or score). including.

Various aspects of the invention include two or more types of CA regions (two or more types of indicator CA regions) for assessing (eg, detecting, diagnosing) HRD in a sample. ) Includes using a composite analysis. Therefore, in one aspect, the invention is a method of assessing (eg, detecting, diagnosing) HRD in a sample and (1) determining the total number (or total length) of indicator LOH regions in the sample. (2) Steps to determine the total number (or total length) of indicator TAI regions in the sample; and (3) Presence of HRD in the sample based at least in part on the decisions made in (1) and (2). Alternatively, a method is provided that includes a step of determining absence (eg, detecting, diagnosing). In another aspect, the invention is a method of assessing (eg, detecting, diagnosing) HRD in a sample, (1) determining the total number (or total length) of indicator LOH regions in the sample; ( 2) Steps to determine the total number (or total length) of indicator LST regions in the sample; and the presence or absence of HRD in the sample, at least in part based on the decisions made in (3) (1) and (2). Provided are methods that include a step of determining (eg, detecting, diagnosing). In another aspect, the invention is a method of assessing (eg, detecting, diagnosing) HRD in a sample, (1) determining the total number (or total length) of indicator TAI regions in the sample; ( 2) Steps to determine the total number (or total length) of indicator LST regions in the sample; and the presence or absence of HRD in the sample, at least in part based on the decisions made in (3) (1) and (2). Provided are methods that include a step of determining (eg, detecting, diagnosing). In another aspect, the invention is a method of assessing (eg, detecting, diagnosing) HRD in a sample, (1) determining the total number (or total length) of indicator LOH regions in the sample; ( 2) Steps to determine the total number of indicator TAI regions in the sample; (3) Steps to determine the total number (or total length) of indicator LST regions in the sample; and in (4) (1), (2) and (3) Provided are methods that include determining (eg, detecting, diagnosing) the presence or absence of HRD in a sample, at least in part based on the decisions made.

Various aspects of the invention involve using a combined analysis of the averages of three different CA regions to evaluate (eg, detect, diagnose) HRD in a sample. Thus, in one aspect, the invention is a method of assessing (eg, detecting, diagnosing) HRD in a sample and (1) a LOH region (eg, eg) having a particular size or characteristic in the sample. Steps to determine the total number of "indicator LOH regions" as defined herein; (2) TAI regions of a particular size or characteristic in a sample (eg, "indicators" as defined herein). Steps to determine the total number of "TAI regions"); (3) Steps to determine the total number of LST regions of a particular size or characteristic in a sample (eg, "indicator LST regions" as defined herein). (4) Steps to calculate the average (eg, arithmetic mean) of the decisions made in (1), (2) and (3); and (5) (4) calculated average (eg, arithmetic) A method is provided that includes a step of assessing HRD in a sample, at least in part based on the average).

As used herein, a "CA region score" is a test value or score (eg, representing or corresponding to it) derived or calculated (eg, representing or corresponding to) from an indicator CA region detected in a sample. , A score or test value derived or calculated from the number of indicator CA regions detected in the sample). Similarly, as used herein, the "LOH region score" is a subset of the CA region score and is derived or calculated from or calculated from the indicator LOH region detected in the sample (eg, representative of it). Or corresponding test values or scores (eg, scores or test values derived or calculated from the number of indicator LOH regions detected in the sample), also for TAI region scores and LST region scores. The same is true. Such a score may, in some embodiments, simply be the number of indicator CA regions detected in the sample. In some embodiments, the score is more complex, with the length of each indicator CA region or a subset of the indicator CA regions detected as a factor.

As discussed above, the present invention generally involves combining the analysis of two or more types of CA region scores, which may include the number of such regions. Therefore, in one aspect, the invention is a method of assessing (eg, detecting, diagnosing) HRD in a sample, (1) determining the LOH region score for the sample; (2) TAI for the sample. Steps to determine region score; and (3) (a) detect (or diagnose) HRD in a sample based at least in part on either the LOH region score above the reference count or the TAI region score above the reference count. ) Step; or optionally (3) (b) Detect (or diagnose) the absence of HRD in the sample, at least in part, based on both the LOH region score not exceeding the reference count and the TAI region score not exceeding the reference count. To provide a method, including the steps. In another aspect, the invention is a method of assessing (eg, detecting, diagnosing) HRD in a sample, in which (1) the step of determining the LOH region score for the sample; (2) the LST region score for the sample. And (3) (a) the step of detecting (or diagnosing) HRD in a sample based at least in part on either the LOH region exceeding the number of references or the LST region score exceeding the number of references; Or optionally (3) (b) the step of detecting (or diagnosing) the absence of HRD in a sample, at least partially based on both the LOH region score not exceeding the number of references and the LST region score not exceeding the number of references. Provides a method including ,. In another aspect, the invention is a method of assessing (eg, detecting, diagnosing) HRD in a sample, in which (1) the step of determining the TAI region score for the sample; (2) the LST region score for the sample. And (3) (a) the step of detecting (or diagnosing) HRD in a sample based at least in part on either the TAI region score above the reference count or the LST region score above the reference count. ; Or optionally (3) (b) detect (or diagnose) the absence of HRD in the sample, at least in part, based on both the TAI region score not exceeding the reference count and the LST region score not exceeding the reference count. Provide methods, including steps. In another aspect, the invention is a method of assessing (eg, detecting, diagnosing) HRD in a sample, in which (1) the step of determining the LOH region score for the sample; (2) the TAI region score for the sample. The stage of determining the The step of detecting (or diagnosing) HRD in a sample based on at least in part; or optionally (4) (b) a LOH region score that does not exceed the number of references, a TAI region score that does not exceed the number of references, and Provided are methods that include a step of detecting (or diagnosing) the absence of HRD in a sample, at least partially based on an LST region score that does not exceed the number of references.

In some embodiments, the CA region score is defined as (1) the detected LOH region (“LOH region score” as defined herein), (2) the detected TAI region (defined herein). Derived or calculated from two or more of the detected LST regions (“LST region scores” as defined herein) and / or (3) detected LST regions (“TAI region scores”). A combination of scores to be (eg, representing or corresponding to it). In some embodiments, the LOH region score and the TAI region score are combined as follows to obtain the CA region score:
CA area score = A ^* (LOH area score) + B ^* (TAI area score)

In some embodiments, the LOH region score and the TAI region score are combined as follows to obtain the CA region score:
CA area score = 0.32 ^* (LOH area score) +0.68 ^* (TAI area score)
Or
CA area score = 0.34 ^* (LOH area score) +0.66 ^* (TAI area score)

In some embodiments, the LOH region score and the LST region score are combined as follows to obtain the CA region score:
CA area score = A ^* (LOH area score) + B ^* (LST area score)

In some embodiments, the LOH region score for a sample and the LST region score for a sample are combined as follows to obtain a CA region score:
CA area score = 0.85 ^* (LOH area score) + 0.15 ^* (LST area score)

In some embodiments, the TAI region score and the LST region score are combined as follows to obtain the CA region score:
CA area score = A ^* (TAI area score) + B ^* (LST area score)

In some embodiments, the LOH region score, the TAI region score and the LST region score are combined as follows to obtain the CA region score:
CA area score = A ^* (LOH area score) + B ^* (TAI area score) + C ^* (LST area score)

In some embodiments, the LOH region score, the TAI region score and the LST region score are combined as follows to obtain the CA region score:
CA area score = 0.21 ^* (LOH area score) +0.67 ^* (TAI area score) +0.12 ^* (LST area score)
Or
CA area score = [0.24] ^* (LOH area score) + [0.65] ^* (TAI area score) + [0.11] ^* (LST area score)
Or
CA area score = [0.11] ^* (LOH area score) + [0.25] ^* (TAI area score) + [0.12] ^* (LST area score)

本明細書中に具体的に例示されたいくつかを含む、いくつかの態様において、これらの係数の1つまたは複数（すなわち、A、B、もしくはC、またはそれらの任意の組み合わせ）は1であり、いくつかの態様においては、3つの係数のすべて（すなわち、A、B、およびC）が1である。したがって、いくつかの態様において、CA領域スコア＝（LOH領域スコア）＋（TAI領域スコア）＋（LST領域スコア）であり、式中、LOH領域スコアはインジケーターLOH領域の数（またはLOHの全長）であり、TAI領域スコアはインジケーターTAI領域の数（またはTAIの全長）であり、LST領域スコアはインジケーターLST領域の数（またはLSTの全長）である。 In some embodiments, the CA region score is obtained from (1) the detected LOH region (“LOH region score” as defined herein), in order to obtain the CA region score from one of the following equations: (2) Detected TAI region (“TAI region score” as defined herein) and / or (3) Detected LST region (“LST region score” as defined herein). A combination of scores derived or calculated (eg, representing or corresponding to it) from the average of (eg, the arithmetic mean):

In some embodiments, including some specifically exemplified herein, one or more of these coefficients (ie, A, B, or C, or any combination thereof) is 1. Yes, in some embodiments, all three coefficients (ie, A, B, and C) are 1. Therefore, in some embodiments, the CA region score = (LOH region score) + (TAI region score) + (LST region score), and in the equation, the LOH region score is the number of indicator LOH regions (or the overall length of the LOH). The TAI region score is the number of indicator TAI regions (or the total length of the TAI), and the LST region score is the number of indicator LST regions (or the total length of the LST).

In some cases, the equation does not have all of the specified coefficients (and therefore does not include the corresponding variables). For example, the embodiment just mentioned may be applied to equation (2) where A in equation (2) is 0.95 and B in equation (2) is 0.61. C and D are considered inapplicable as these coefficients and their corresponding variables are not found in equation (2) (clinical variables are incorporated into the clinical score found in equation (2)). Although). In some embodiments, A is 0.9 to 1, 0.9 to 0.99, 0.9 to 0.95, 0.85 to 0.95, 0.86 to 0.94, 0.87 to 0.93, 0.88 to 0.92, 0.89 to 0.91, 0.85 to 0.9, 0.8 to 0.95, 0.8 to It is 0.9, 0.8 to 0.85, 0.75 to 0.99, 0.75 to 0.95, 0.75 to 0.9, 0.75 to 0.85, or 0.75 to 0.8. In some embodiments, B is 0.40 to 1, 0.45 to 0.99, 0.45 to 0.95, 0.55 to 0.8, 0.55 to 0.7, 0.55 to 0.65, 0.59 to 0.63, or 0.6 to 0.62. In some embodiments, C is 0.9-1, 0.9 to 0.99, 0.9 to 0.95, 0.85 to 0.95, 0.86 to 0.94, 0.87 to 0.93, 0.88 to 0.92, 0.89 to 0.91, 0.85 to 0.9, where applicable. It is 0.8 to 0.95, 0.8 to 0.9, 0.8 to 0.85, 0.75 to 0.99, 0.75 to 0.95, 0.75 to 0.9, 0.75 to 0.85, or 0.75 to 0.8. In some embodiments, D is 0.9-1, 0.9 to 0.99, 0.9 to 0.95, 0.85 to 0.95, 0.86 to 0.94, 0.87 to 0.93, 0.88 to 0.92, 0.89 to 0.91, 0.85 to 0.9, where applicable. It is 0.8 to 0.95, 0.8 to 0.9, 0.8 to 0.85, 0.75 to 0.99, 0.75 to 0.95, 0.75 to 0.9, 0.75 to 0.85, or 0.75 to 0.8.

In some embodiments, A is 0.1 and 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, 8 , 9, 10, 11, 12, 13, 14, 15 or 20; or 0.2 and 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 1.5, 2, 2.5, 3, 3.5, 4 , 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or 20; or between 0.3 and 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 1.5, 2 , 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or 20; or between 0.4 and 0.5, 0.6, 0.7, 0.8, 0.9 , 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or 20; or between 0.5 and 0.6, 0.7 , 0.8, 0.9, 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or 20; or 0.6 And 0.7, 0.8, 0.9, 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or 20; Or between 0.7 and 0.8, 0.9, 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or 20; Or between 0.8 and 0.9, 0.9, 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or 20; or 0.9 And 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or 20; or 1 and 1.5, 2 , 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or 20; or between 1.5 and 2, 2.5, 3, 3.5, 4 , 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or 20; or between 2 and 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, 8 , 9, 10, 11, 12, 13, 14, 15 or 20; or 2.5 and 3, 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14 , 15 if Or between 3 and 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or 20; or between 3.5 and 4, 4.5, Between 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or 20; or between 4 and 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, Between 14, 15 or 20; or between 4.5 and 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or 20; or between 5 and 6, 7, 8, 9, Between 10, 11, 12, 13, 14, 15 or 20; or between 6 and 7, 8, 9, 10, 11, 12, 13, 14, 15 or 20; or between 7 and 8, 9, Between 10, 11, 12, 13, 14, 15 or 20; or between 8 and 9, 10, 11, 12, 13, 14, 15 or 20; or between 9 and 10, 11, 12, 13, Between 14, 15 or 20; or between 10 and 11, 12, 13, 14, 15 or 20; or between 11 and 12, 13, 14, 15 or 20; or between 12 and 13, 14, Between 15 or 20; or between 13 and 14, 15 or 20; or between 14 and 15 or 20; or between 15 and 20; B is between 0.1 and 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or 20 Between; or 0.2 and 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11, Between 12, 13, 14, 15 or 20; or 0.3 and 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, Between 8, 9, 10, 11, 12, 13, 14, 15 or 20; or between 0.4 and 0.5, 0.6, 0.7, 0.8, 0.9, 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, Between 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or 20; or between 0.5 and 0.6, 0.7, 0.8, 0.9, 1, 1.5, 2, 2.5, 3, 3.5, Between 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or 20; or between 0.6 and 0.7, 0.8, 0.9, 1, 1.5, Between 2, 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or 20; or 0.7 and 0.8, 0.9, 1, 1.5, Between 2, 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or 20; or between 0.8 and 0.9, 1, 1.5, 2, Between 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or 20; or between 0.9 and 1, 1, 1.5, 2, 2.5, 3, Between 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or 20; or between 1 and 1.5, 2, 2.5, 3, 3.5, 4, 4.5, Between 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or 20; or between 1.5 and 2, 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, 8, Between 9, 10, 11, 12, 13, 14, 15 or 20; or between 2 and 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, Between 14, 15 or 20; or between 2.5 and 3, 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or 20; or 3 and Between 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or 20; or between 3.5 and 4, 4.5, 5, 6, 7, 8, 9, Between 10, 11, 12, 13, 14, 15 or 20; or between 4 and 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or 20; or Between 4.5 and 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or 20; or between 5 and 6, 7, 8, 9, 10, 11, 12, 13, 14, Between 15 or 20; or between 6 and 7, 8, 9, 10, 11, 12, 13, 14, 15 or 20; or between 7 and 8, 9, 10, 11, 12, 13, 14, Between 15 or 20; or between 8 and 9, 10, 11, 12, 13, 14, 15 or 20; or between 9 and 10, 11, 12, 13, 14, 15 or 20; or Between 10 and 11, 12, 13, 14, 15 or 20; or between 11 and 12, 13, 14, 15 or 20; or between 12 and 13, 14, 15 or 20; or 13 and Between 14, 15 or 20; or between 14 and 15 or 20 Between; or between 15 and 20; C is 0.1 and 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 1.5, 2, 2.5, 3, 3.5, where applicable. , 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or 20; or between 0.2 and 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1 , 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or 20; or between 0.3 and 0.4, 0.5, 0.6 , 0.7, 0.8, 0.9, 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or 20; Or 0.4 and 0.5, 0.6, 0.7, 0.8, 0.9, 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 Or between 20; or 0.5 and 0.6, 0.7, 0.8, 0.9, 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13 , 14, 15 or 20; or 0.6 and 0.7, 0.8, 0.9, 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12 , 13, 14, 15 or 20; or 0.7 and 0.8, 0.9, 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12 , 13, 14, 15 or 20; or 0.8 and 0.9, 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13 , 14, 15 or 20; or 0.9 and 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 Or between 20; or between 1 and 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or 20; Or between 1.5 and 2, 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or 20; or between 2 and 2.5, 3, 3.5 , 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or 20; or between 2.5 and 3, 3.5, 4, 4.5, 5, 6, 7, 8 , 9, 10, 11 , 12, 13, 14, 15 or 20; or between 3 and 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or 20; Or between 3.5 and 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or 20; or between 4 and 4.5, 5, 6, 7, 8, 9, 10 , 11, 12, 13, 14, 15 or 20; or between 4.5 and 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or 20; or between 5 and 6 , 7, 8, 9, 10, 11, 12, 13, 14, 15 or 20; or between 6 and 7, 8, 9, 10, 11, 12, 13, 14, 15 or 20; Or between 7 and 8, 9, 10, 11, 12, 13, 14, 15 or 20; or between 8 and 9, 10, 11, 12, 13, 14, 15 or 20; or between 9 and 10. , 11, 12, 13, 14, 15 or 20; or between 10 and 11, 12, 13, 14, 15 or 20; or between 11 and 12, 13, 14, 15 or 20; Or between 12 and 13, 14, 15 or 20; or between 13 and 14, 15 or 20; or between 14 and 15 or 20; or between 15 and 20; and D , If applicable, 0.1 and 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, 8, 9, Between 10, 11, 12, 13, 14, 15 or 20; or 0.2 and 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, Between 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or 20; or between 0.3 and 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 1.5, 2, 2.5, Between 3, 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or 20; or between 0.4 and 0.5, 0.6, 0.7, 0.8, 0.9, 1, Between 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or 20; or between 0.5 and 0.6, 0.7, 0.8, Between 0.9, 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or 20; Or 0.6 and 0.7, 0.8, 0.9, 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or 20 Between; or 0.7 and 0.8, 0.9, 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or 20 Between 0.8 and 0.9, 1,1.5,2,2.5,3,3.5,4,4.5,5,6,7,8,9,10,11,12,13,14,15 or 20; Or between 0.9 and 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or 20; or between 1 and 1.5 , 2, 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or 20; or between 1.5 and 2, 2.5, 3, 3.5 , 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or 20; or between 2 and 2.5, 3, 3.5, 4, 4.5, 5, 6, 7 , 8, 9, 10, 11, 12, 13, 14, 15 or 20; or 2.5 and 3, 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13 Between 14, 15 or 20; or between 3 and 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or 20; or between 3.5 and 4 , 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or 20; or between 4 and 4.5, 5, 6, 7, 8, 9, 10, 11, 12 , 13, 14, 15 or 20; or 4.5 and 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or 20; or 5 and 6, 7, 8 , 9, 10, 11, 12, 13, 14, 15 or 20; or 6 and 7, 8, 9, 10, 11, 12, 13, 14, 15 or 20; or 7 and 8 Between 9, 10, 11, 12, 13, 14, 15 or 20; or between 8 and 9, 10, 11, 12, 13, 14, 15 or 20; or between 9 and 10, 11, 12 , 13, 14, 15 or 20; or between 10 and 11, 12, 13, 14, 15 or 20; or between 11 and 12, 13, 14, 15 or 20; or 12 and 13 Between 14, 15 or 20; or between 13 and 14, 15 Or between 20; or between 14 and 15 or 20; or between 15 and 20. In some embodiments, A, B, and / or C are within the rounding value range of any of these values (eg, A is between 0.45 and 0.54, etc.).

Therefore, in one aspect, the invention is a method of assessing (eg, detecting, diagnosing) HRD in a sample, (1) determining the LOH region score for the sample; (2) TAI for the sample. Steps to determine region score; and (3) (a) detect HRD in a sample based at least in part on a combination of LOH region score and TAI region score that exceeds the number of references (eg, composite CA region score) ( (Or diagnose) stage; or optionally (3) (b) absence of HRD in the sample based at least in part on the combination of LOH region score and TAI region score (eg, composite CA region score) not exceeding the number of references. Provided is a method including a step of detecting (or diagnosing). In another aspect, the invention is a method of assessing (eg, detecting, diagnosing) HRD in a sample, in which (1) the step of determining the LOH region score for the sample; (2) the LST region score for the sample. And (3) (a) detect (or diagnose) HRD in a sample based at least in part on a combination of LOH and LST region scores that exceeds the number of references (eg, composite CA region score). Detect the absence of HRD in the sample, at least partially based on the combination of LOH region score and LST region score (eg, composite CA region score) that does not exceed (3) (b) references. Provide a method including a step of (or diagnosing). In another aspect, the invention is a method of assessing (eg, detecting, diagnosing) HRD in a sample, in which (1) the step of determining the TAI region score for the sample; (2) the LST region score for the sample. And (3) (a) detect (or diagnose) HRD in a sample based at least in part on a combination of TAI region score and LST region score that exceeds the number of references (eg, composite CA region score). Detect the absence of HRD in the sample, at least partially based on the combination of TAI region score and LST region score (eg, composite CA region score) that does not exceed (3) (b) references. Provide a method including a step of (or diagnosing). In another aspect, the invention is a method of assessing (eg, detecting, diagnosing) HRD in a sample, in which (1) the step of determining the LOH region score for the sample; (2) the TAI region score for the sample. (3) Determining the LST region score for a sample; and (4) (a) A combination of LOH region score, TAI region score and LST region score that exceeds the number of references (eg, composite CA region score). The step of detecting (or diagnosing) HRD in a sample based on at least in part; or optionally (4) (b) LOH region score, TAI region score and LST region score (eg, composite) not exceeding the number of references. Provided are methods that include a step of detecting (or diagnosing) the absence of HRD in a sample, at least in part based on the CA region score).

Therefore, another aspect of the invention is a method of assessing (eg, detecting, diagnosing) HRD in a sample, (1) a LOH region having a particular size or characteristic in the sample (eg, the present invention). Steps to determine the total number of "indicator LOH regions" as defined herein; (2) TAI regions of a particular size or characteristic in a sample (eg, "indicator TAI" as defined herein). Steps to determine the total number of "regions"); (3) Steps to determine the total number of LST regions of a particular size or characteristic in a sample (eg, "indicator LST regions" as defined herein); (4) The step of calculating the average of the decisions made in (1), (2) and (3) (eg, the arithmetic mean); and the calculated mean obtained in (5) and (4) (eg, the arithmetic mean). ) Shall include a step of assessing HRD in a sample, at least in part.

In some embodiments, the references (or indexes) discussed above with respect to the CA region score (eg, the number of indicator CA regions) are 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, It may be 15, 16, 18, 19, 20 or more, preferably 5, preferably 8, more preferably 9 or 10, and most preferably 10. References for the total (eg, total) length of the indicator CA region are approximately 75, 90, 105, 120, 130, 135, 150, 175, 200, 225, 250, 275, 300, 325 350, 375, 400, 425, 450, 475, 500 megabases or above, preferably about 75 megabases or above, preferably about 90 or 105 megabases or above, more preferably about 120 or 130 megabases or above. It may be above, more preferably about 135 megabases or above, and most preferably about 150 megabases or above. In some embodiments, the references discussed above with respect to the composite CA region score (eg, the sum of the indicator LOH region, indicator, TAI region and / or indicator LST region) are 5, 6, 7, 8, 9, 10 , 11, 12, 13, 14, 15, 16, 18, 19, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50 or those It may be more than 5, preferably 5, preferably 15, preferably 20, preferably 25, preferably 30, preferably 35, preferably 40 to 44, and most preferably 42 or more. References for the total (eg, combined) length of the indicator LOH region, indicator TAI region and / or indicator LST region are approximately 75, 90, 105, 120, 130, 135, 150, 175, 200, 225, 250. , 275, 300, 325 350, 375, 400, 425, 450, 475, 500 megabases or better, preferably about 75 megabases or better, preferably about 90 or 105 megabases or better, and more It may preferably be at or above about 120 or 130 megabases, more preferably about 135 megabases or above, and most preferably about 150 megabases or above.

In some embodiments, the invention provides a method of detecting an HRD signature in a sample. Therefore, another aspect of the invention is a method of detecting an HRD signature in a sample, (1) a LOH region having a particular size or characteristic in the sample (eg, defined herein ". Steps to determine the total number of "indicator LOH regions"); (2) determine the total number of TAI regions of a particular size or characteristic in a sample (eg, "indicator TAI regions" as defined herein). Steps; (3) Determine the total number of LST regions with a particular size or characteristic in the sample (eg, "indicator LST regions" as defined herein); (4) (1), ( Steps of combining the decisions made in 2) and (3) (eg, calculating or deriving the composite CA region score); and (5) samples with a composite CA region score greater than the reference value, with the HRD signature. It then provides a method that includes a characterization step. In some embodiments, the reference value is 42. Therefore, in some embodiments, the sample is characterized as having an HRD signature when the reference value is 42. In some embodiments, the number of references discussed above with respect to the composite CA region score (eg, the sum of the indicator LOH region, indicator, TAI region and / or indicator LST region) is 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50 or It may be a larger value, preferably 5, preferably 10, preferably 15, preferably 20, preferably 25, preferably 30, preferably 35, preferably 40 to 44, and most often. It may be preferably 42 or more.

In some embodiments, the number of indicator CA regions (or total length, CA region score or composite CA region score) in the sample is at least 2x, 3x, 4x, 5x, 6x, that is more than the reference. A 7x, 8x, 9x or 10x larger is considered "greater" than the reference, and in some embodiments it is at least 1 standard deviation, 2 standard deviations, 3 standard deviations, 4 times larger than the reference. If the standard deviation, 5 standard deviation, 6 standard deviation, 7 standard deviation, 8 standard deviation, 9 standard deviation or 10 standard deviation is greater, it is considered "greater than". Conversely, in some embodiments, the number of indicator CA regions (or total length, CA region score or composite CA region score) in the sample is 2x, 3x, 4x, 5x, 6 times that of the reference. If it is not times, 7 times, 8 times, 9 times or 10 times larger, it is considered "not larger" than the reference, and in some embodiments, 1 standard deviation, 2 standard deviations, 3 Standard Deviation, 4 Standard Deviation, 5 Standard Deviation, 6 Standard Deviation, 7 Standard Deviation, 8 Standard Deviation, 9 Standard Deviation or 10 Standard Deviation If not greater, it is determined to be "not greater".

In some embodiments, the number of references (or length, value or score) is derived from a valid reference group. Such reference populations include (a) patients with the same cancer as the patients being tested, (b) patients with the same cancer subtype, (c) similar genetic or other clinical or molecular features. Patients with cancer who have cancer, (d) patients who responded to a particular treatment, (e) patients who did not respond to a particular treatment, (f) patients who are apparently healthy (eg, do not have any cancer? Or at least patients who do not have cancer in the patients being tested) and the like. The number of references (or length, value or score) may be representative of (a) the number (or length, value or score) recognized as a whole in the reference population, and (b) as a whole or in the reference population. It may be the average of the numbers (or lengths, values or scores) found in a particular subpopulation (mean, median, etc.), and (c) (i) their respective numbers. Rank by (or length, value or score) or (ii) clinical features found to have (eg, response intensity, prognosis (including time to cancer-specific death), etc.) Numbers (or lengths, values or scores) that are recognized as trisections, quadrants, quintuplets, etc. of the reference population (eg, average, eg mean). Or may be representative of (median, etc.), or (d) be highly sensitive to detect HRD to predict response to a particular treatment (eg, platinum, PARP inhibitor, etc.). May be selected.

In some embodiments, the reference or index indicates that the HRD is the same as the reference if it is exceeded by the test value or score from the sample, and if it is not exceeded by the test value or score from the sample, the HRD ( Or it indicates that there is no functional HDR). In some embodiments, they are different.

In another aspect, the invention provides a method of predicting the status of the BRCA1 and BRCA2 genes in a sample. Such a method is similar to the method described above, but the determination of the CA region, LOH region, TAI region, LST region, or a score incorporating them assesses BRCA1 and / or BRCA2 deficiency in the sample ( For example, it is different in that it is used for detecting).

In another aspect, the invention provides a method of predicting the response of a cancer patient to a cancer treatment regimen that includes a DNA damaging agent, anthracycline, topoisomerase I inhibitor, radiation, and / or PARP inhibitor. Such a method is similar to the above method, but with a CA region, LOH region, TAI region, LST region, or a score that incorporates them (high HRD score (eg, HRD signature or high combined CA region score)). Is used to predict the likelihood that a cancer patient will respond to a cancer treatment regimen.

In some embodiments, the patient is an untreated patient. In another aspect, the invention provides a method of treating cancer. Such methods are similar to those described above, but with specific treatment regimens based at least in part on determining the CA region, LOH region, TAI region, LST region, or a score that incorporates them. It differs in that it is given (recommended, prescribed, etc.).

In another aspect, the invention is in a patient identified as having (or having) cancer cells determined to have the high levels of HRD described herein (eg, HRD signature). It is characterized by the use of one or more drugs selected from the group consisting of DNA damage agents, anthracyclines, topoisomerase I inhibitors and PARP inhibitors in the manufacture of drugs useful for treating cancer.

In another aspect, this document features a method for evaluating a sample for the presence of mutations in a gene derived from the HDR pathway. Such a method is similar to the method described above, but the determination of the CA region, LOH region, TAI region, LST region, or a score incorporating them is the presence of mutations in the gene derived from the HDR pathway ( Or absent) in that it is used to detect.

In another aspect, this document features a method for assessing a patient's cancer cells for the presence of an HRD signature. The method has (a) the step of detecting the presence of an indicator CA region above the reference number in at least one pair of human chromosomes of a cancer patient's cancer cell, and (b) the patient having a cancer cell with an HRD signature. Includes or essentially consists of steps to identify as. In another aspect, this document features a method for assessing a patient's cancer cells for the presence of an HDR-deficient state. The method has (a) the step of detecting the presence of an indicator CA region that exceeds the number of references in at least one pair of human chromosomes of a cancer patient's cancer cell, and (b) the patient having a cancer cell with an HDR-deficient state. Includes or essentially consists of steps to identify as. In another aspect, this document features a method for assessing a patient's cancer cells for having an HRD signature. The method has (a) the step of detecting the presence of an indicator CA region above the reference number in at least one pair of human chromosomes of a cancer patient's cancer cell, and (b) the patient having cancer cells with an HRD signature. It then includes or becomes essentially from these stages of identification. In another aspect, this document features a method for assessing a patient's cancer cells for the presence of gene mutations within genes derived from the HDR pathway. The method has (a) the step of detecting the presence of an indicator CA region above the reference number in at least one pair of human chromosomes of a cancer patient's cancer cell, and (b) the patient having a cancer cell with a gene mutation. Includes or essentially consists of steps to identify as.

In another aspect, the document responds to a cancer treatment regimen that involves the patient administering radiation or a drug selected from the group consisting of DNA damaging agents, anthracyclines, topoisomerase I inhibitors and PARP inhibitors. It features a method for determining whether or not a probability is high. The method is likely to (a) detect the presence of an indicator CA region that exceeds the number of references in at least one pair of human chromosomes in a cancer patient's cancer cell, and (b) make the patient respond to a cancer treatment regimen. Includes or essentially consists of steps to identify as. In another aspect, this document features a method for assessing a patient. The method is (a) a step in determining that a patient contains cancer cells bearing the HRD signature, due to the presence of an indicator CA region that exceeds the number of references in at least one pair of human chromosomes of the cancer patient's cancer cells. It includes, or consists essentially of, a stage in which the cancer cells are indicated to have an HRD signature, and (b) a stage in which the patient is diagnosed as having a cancer cell with an HRD signature. In another aspect, this document features a method for assessing a patient. The method is (a) a step of determining that a patient contains cancer cells with an HDR-deficient state, due to the presence of an indicator CA region that exceeds the number of references in at least one pair of human chromosomes of the cancer patient's cancer cells. Includes, or consists of, a stage in which the cancer cells are indicated to have an HDR-deficient state, and (b) a stage in which the patient is diagnosed with a cancer cell with an HDR-deficient state. In another aspect, this document features a method for assessing a patient. The method is (a) a step of determining that a patient contains cancer cells with an HDR-deficient state, due to the presence of an indicator CA region that exceeds the number of references in at least one pair of human chromosomes of the cancer patient's cancer cells. Includes, or consists of, a stage in which the cancer cells are indicated to have high HDR, and (b) a stage in which the patient is diagnosed with cancer cells with an HDR-deficient state. In another aspect, this document features a method for assessing a patient. The method (a) is the step of determining that a patient contains a cancer cell having a gene mutation in a gene derived from the HDR pathway, in which the number of references in at least one pair of human chromosomes of the cancer cell of the cancer patient is determined. The presence of an over indicator CA region comprises or includes a step indicating that the cancer cell has a gene mutation, and (b) diagnosing the patient as having a cancer cell with a gene mutation. From stage to essential. In another aspect, the document responds to a cancer treatment regimen that involves administering to a patient a drug selected from the group consisting of radiation or DNA damage agents, anthracyclines, topoisomerase I inhibitors and PARP inhibitors. It features a method for assessing potential. The method is (a) a step in determining that a patient contains cancer cells bearing the HRD signature, due to the presence of an indicator CA region that exceeds the number of references in at least one pair of human chromosomes of the cancer patient's cancer cells. Includes a step in which the cancer cell is indicated to have an HRD signature, and (b) a step in diagnosing the patient as likely to respond to a cancer treatment regimen, at least in part based on the presence of the HRD signature. Or, from these stages it becomes essential. In another aspect, the document responds to a cancer treatment regimen that involves the patient administering radiation or a drug selected from the group consisting of DNA damaging agents, anthracyclines, topoisomerase I inhibitors and PARP inhibitors. It features a method for assessing potential. The method is (a) a step in determining that a patient contains cancer cells bearing the HRD signature, due to the presence of an indicator CA region that exceeds the number of references in at least one pair of human chromosomes of the cancer patient's cancer cells. Includes a step in which the cancer cells are indicated to have the HRD signature, and (b) a step in diagnosing the patient as likely to respond to the cancer treatment regimen, at least in part based on the presence of the HRD signature. Or it becomes essential from these stages.

In another aspect, this document features a method for performing a diagnostic analysis of a patient's cancer cells. The method (a) detects the presence of an indicator CA region above the reference number in at least one pair of human chromosomes of the cancer cell, and (b) identifies or identifies the patient as having the cancer cell with the HRD signature. Includes or is essentially from these stages. In another aspect, this document features a method for performing a diagnostic analysis of a patient's cancer cells. The method (a) detects the presence of more indicator CA regions on at least one pair of human chromosomes of cancer cells, and (b) identifies the patient as having cancer cells with HDR deficiency. Or it includes or is essentially from these stages. In another aspect, this document features a method for performing a diagnostic analysis of a patient's cancer cells. The method (a) detects the presence of more indicator CA regions on at least one pair of human chromosomes of cancer cells, and (b) identifies the patient as having cancer cells with HDR deficiency. Or it includes or is essentially from these stages. In another aspect, this document features a method for performing a diagnostic analysis of a patient's cancer cells. The method involves (a) detecting the presence of an indicator CA region that exceeds the number of references in at least one pair of human chromosomes of cancer cells, which is relatively long, and (b) the patient within a gene derived from the HDR pathway. Includes or consists essentially of the steps of identifying or classifying cancer cells with a gene mutation in. In another aspect, the document responds to a cancer treatment regimen involving cancer patients receiving radiation or a drug selected from the group consisting of DNA damaging agents, anthracyclines, topoisomerase I inhibitors and PARP inhibitors. It features a method for performing a diagnostic analysis of a patient's cancer cells to determine if they are likely to do so. The method identifies (a) the step of detecting the presence of an indicator CA region above the number of references in at least one pair of human chromosomes of cancer cells, and (b) identifying patients as likely to respond to a cancer treatment regimen. Or it includes or is essentially from these stages.

In another aspect, the document features a method for diagnosing a patient as having cancer cells bearing the HRD signature. The method is (a) a step in determining that a patient contains cells bearing the HRD signature, which is due to the presence of an indicator CA region that exceeds the number of references in at least one pair of human chromosomes in the cancer cells of the cancer patient. It includes, or consists essentially of, a stage in which the cancer cells are indicated to have an HRD signature, and (b) a stage in which the patient is diagnosed with a cancer cell with an HRD signature. In another aspect, the document features a method for diagnosing a patient as having cancer cells with an HDR deficient state. The method is (a) a step of determining that a patient contains cancer cells with an HDR-deficient state, due to the presence of an indicator CA region that exceeds the number of references in at least one pair of human chromosomes of the cancer patient's cancer cells. Includes, or consists of, a stage in which the cancer cells are indicated to have an HDR-deficient state, and (b) a stage in which the patient is diagnosed with a cancer cell with an HDR-deficient state. In another aspect, the document features a method for diagnosing a patient as having cancer cells with an HDR deficient state. The method is (a) a step of determining that a patient contains cancer cells with an HDR-deficient state, due to the presence of an indicator CA region that exceeds the number of references in at least one pair of human chromosomes of the cancer patient's cancer cells. Includes, or becomes essentially from these stages, the stage in which the cancer cell is indicated to have an HDR deficient state, and (b) the stage in which the patient is diagnosed as having a cancer cell with an HDR deficient state. .. In another aspect, the document features a method for diagnosing a patient as having a cancer cell with a gene mutation within a gene derived from the HDR pathway. The method is (a) a step of determining that a patient contains a cancer cell carrying a gene mutation, due to the presence of an indicator CA region that exceeds the number of references in at least one pair of human chromosomes of the cancer cell of the cancer patient. , A step in which a cancer cell is indicated to have a gene mutation, and (b) a step of diagnosing a patient as having a cancer cell with a gene mutation, or consists essentially of these steps. In another aspect, this document is a candidate for a cancer treatment regimen that involves administering to a patient a drug selected from the group consisting of radiation or DNA damage agents, anthracyclines, topoisomerase I inhibitors and PARP inhibitors. It features a method for diagnosing the presence. The method is (a) a step in determining that a patient contains cancer cells bearing the HRD signature, due to the presence of an indicator CA region that exceeds the number of references in at least one pair of human chromosomes of the cancer patient's cancer cells. Includes a step in which the cancer cell is indicated to have an HRD signature, and (b) a step in diagnosing the patient as likely to respond to a cancer treatment regimen, at least in part based on the presence of the HRD signature. Or, from these stages it becomes essential. In another aspect, this document is a candidate for a cancer treatment regimen that involves administering to a patient a drug selected from the group consisting of radiation or DNA damage agents, anthracyclines, topoisomerase I inhibitors and PARP inhibitors. It features a method for diagnosing the presence. The method is (a) a step of determining that a patient contains cancer cells with a high HRD signature, due to the presence of an indicator CA region that exceeds the number of references in at least one pair of human chromosomes of the cancer patient's cancer cells. , The stage in which the cancer cell is indicated to have the HRD signature, and (b) the stage in which the patient is diagnosed as likely to respond to the cancer treatment regimen, at least in part based on the presence of the HRD signature. Including or becoming essential from these stages.

In another aspect, the invention provides a method for evaluating a patient. The method (a) determines whether a patient has (or has) cancer cells that exceed the number of references in the CA region (or, eg, a CA region score that exceeds the reference CA region score); and ( b) (1) If the patient is determined to have (or have) cancer cells that exceed the number of references in the CA region (or, for example, a CA region score that exceeds the reference CA region score), the patient is associated with HRD. The stage of diagnosing with cancer cells; or (b) (2) the patient does not have (or has never had) more cancer cells than the number of references in the CA region (or, for example, the patient has a reference CA region score. Includes or includes the stage of diagnosing a patient as having no cancer cells with HRD if it is determined to have (or never had) cancer cells with a CA region score greater than From stage to essential.

In another aspect, the invention is useful for determining the total or total length of CA regions in at least one pair of chromosomes (or DNA derived from it) in a sample obtained from a cancer patient, and (a). HRD, high HRD, or probable HRD in the sample (eg, HRD signature, respectively), (b) deficiency (or probable deficiency) in the BRCA1 or BRCA2 gene in the sample, or (c) cancer patients are DNA-damaging agents Multiple polymorphic regions of human genomic DNA in the manufacture of diagnostic kits that are also useful for detecting a high likelihood of responding to a cancer treatment regimen, including anthracyclins, topoisomerase I inhibitors, radiation, or PARP inhibitors. It is characterized by the use of multiple oligonucleotides capable of hybridizing with.

In another aspect, the invention features a system for detecting HRD (eg, HRD signature) in a sample. The system is based on (a) a sample analyzer configured to generate multiple signals for genomic DNA of at least one pair of human chromosomes (or DNA derived from it) in a sample, and (b) multiple signals. Includes, or consists essentially of, a computer subsystem programmed to calculate the number or total length of CA regions in at least one pair of human chromosomes. The computer subsystem compares the number of CA regions or the total length to the number of references, (a) the probability of HRD, high HRD, or HRD in the sample (eg, HRD signature), and (b) the BRCA1 gene in the sample. Or a BRCA2 gene deficiency (or probable deficiency), or (c) cancer patients are more likely to respond to a cancer treatment regimen that includes DNA inhibitors, anthracyclines, topoisomerase I inhibitors, radiation, or PARP inhibitors. Can be programmed to detect. The system may include an output module configured to display (a), (b) or (c). The system may include an output module configured to display recommendations for the use of cancer treatment regimens.

In another aspect, the invention, when performed on a computer, is any CA region (the CA region is optionally an indicator) that resides on one or more human chromosomes other than the human X and Y sex chromosomes. A computer program product incorporated into a computer-readable medium to detect the presence or absence of a) CA region; and to give instructions to determine the total or total length of the CA region on one or more pairs of chromosomes. provide. The computer program product may contain other instructions.

In another aspect, the invention provides a diagnostic kit. The kit includes, or is essentially derived from, at least 500 oligonucleotides capable of hybridizing to multiple polymorphic regions of human genomic DNA (or DNA derived from it); and the computer program products provided herein. Become a target. Computer program products may be integrated into a computer-readable medium and, when run on a computer, any CA region that resides on one or more of human chromosomes other than the human X and Y sex chromosomes ( CA regions are optionally indicator CA regions) to detect the presence or absence; and give instructions to determine the total or total length of CA regions in one or more pairs of chromosomes. The computer program product may contain other instructions.

In any one or more aspects of the aspects of the invention described in the preceding paragraph, any one or more of the following may be applied as appropriate. The CA region can be determined on at least 2, 5, 10 or 21 pairs of human chromosomes. The cancer cells may be ovarian cancer cells, breast cancer cells, lung cancer cells or esophageal cancer cells. The number of references may be 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18 or 20, or more. Human chromosome 17 can be excluded from at least one pair of human chromosomes. The DNA damaging agent may be cisplatin, carboplatin, oxalaplatin, or picoplatin, the anthracycline may be epirubincin or doxorubicin, and the topoisomerase I inhibitor may be campothecin, topotecan or irinotecan. Or the PARP inhibitor may be iniparib, olaparib or velapirib. The patient may be an untreated patient.

As described herein, a sample (eg, a cancer cell sample, or a sample containing DNA from one or more cancer cells) has the genome of the cell being evaluated as (a) a reference number. If it contains either a LOH region score that exceeds, a TAI region score or an LST region score, or (b) a composite CA region score that exceeds the number of references, it is referred to as an "HRD signature" (or alternatively referred to as an "HDR-deficient signature"). Can be identified as having. Conversely, a sample (eg, a cancer cell sample, or a sample containing DNA from one or more cancer cells) has a LOH region score in which the genome of the cell being evaluated does not (a) exceed the number of references, respectively. , TAI region score and LST region score, or (b) if it contains a composite CA region score that does not exceed the number of references, identify it as lacking the "HRD signature" (or alternatively referred to as the "HDR-deficient signature"). Can be done.

Cells identified as having the HRD signature (eg, cancer cells) can be classified as likely to have an HDR deficiency and / or a deficiency of one or more genes in the HDR pathway. it can. For example, cancer cells identified as having the HRD signature can be classified as likely to have an HDR-deficient state. In some cases, cancer cells identified as having the HRD signature can also be classified as likely to have a defect in one or more genes in the HDR pathway. As used herein, a deficient state with respect to a gene means that the sequence, structure, expression and / or activity of the gene or its product is deficient as compared to normal. Examples include, but are not limited to, low or no expression of mRNA or protein, harmful mutations, overmethylation, reduced activity (eg, enzymatic activity, ability to bind to another biomolecule), etc. included. As used herein, a deficient state for a pathway (eg, the HDR pathway) means that at least one gene (eg, BRCA1) in that pathway is deficient. Examples of highly harmful mutations include frameshift mutations, stop codon mutations, and mutations that lead to altered RNA splicing. Gene deficiency in the HDR pathway can result in deficiency or reduced activity of homologous recombination repair in cancer cells. Examples of genes in the HDR pathway include, but are not limited to, the genes listed in Table 1.

(Table 1) Selected HDR pathway genes

As described herein, identification of the CA locus (as well as the size and number of CA regions) primarily involves genotyping the sample at various genomic loci (eg, SNP loci, large-scale sequencing). Determined by the individual bases in) and, secondly, may include determining whether the locus exhibits either LOH, TAI or LST. Any suitable technique can be used to genotype at the locus of interest within the cell's genome. For example, single nucleotide polymorphism (SNP) arrays (eg, human genome-wide SNP arrays), targeted sequencing of loci of interest (eg, sequencing of SNP loci and their surrounding sequences), and even large-scale sequencing. Even singles (eg, whole exome, transcriptome, or genome sequencing) can be used to identify loci as homozygous or heterozygous. Typically, the length of the CA region can be determined by performing a locus homozygous or heterozygous analysis over a length of the chromosome. For example, by evaluating a series of SNP positions spaced apart from each other in the length direction of the chromosome (eg, located at intervals of about 25 kb to about 100 kb) using the results of the SNP array, the chromosomes Not only the presence of a homozygous region (eg, LOH) that exists in the length direction, but also the length of that region can be determined. The results from the SNP array can be used to create a graph plotting the amount of alleles along the length of the chromosome. Allele amount d _i relates SNPi, can be calculated from the adjustment signal intensity of the two alleles (A _i and _{B i): d i = A} i / (A i + B i). Examples of such graphs are presented in Figures 1 and 2, which show the differences between fresh frozen samples and FFPE samples, and the differences between SNP microarray analysis and SNP sequencing analysis. A large number of variants on nucleic acid arrays useful in the present invention are known in the art. These include the arrays used in the various examples below (eg, the Affymetrix 500K GeneChip array in Example 3; the Affymetrix OncoScan ™ FFPE Express 2.0 Services (formerly MIP CN Services) in Example 4). ..

Once the sample is genotyped for multiple loci (eg, SNPs), common techniques can be used to identify loci and regions of LOH, TAI and LST (International Application No. PCT). / US2011 / 040953 (published as WO / 2011/160063); International application No. PCT / US2011 / 048427 (published as WO / 2012/02724); Popova et al., Ploidy and large-scale genomic instability consistently identify basal-like breast carcinomas with BRCA1 / 2 inactivation, CANCER RES. (2012) 72: 5454-5462). In some embodiments, determining chromosomal imbalances or large-scale transitions includes determining whether they are somatic or germline abnormalities. One way to do this is to compare the somatic genotype with the germline. For example, genotypes for multiple loci (eg, SNPs) can be determined in both germline (eg, blood) and somatic (eg, tumor) samples. The genotypes of each sample can be compared (typically by computer calculation) to determine where the germline cell genome is heterozygous and the somatic cell genome is homozygous. Such a locus is the LOH locus, and the region of such a locus is the LOH region.

Computer computation can also be used to determine if the abnormality is germline or somatic. Such techniques are particularly useful when germline samples for analysis and comparison are not available. For example, the LOH region can be detected using information from SNP arrays by using algorithms such as those described elsewhere (Nannya et al., Cancer Res. (2005) 65: 6071-6079 (Nannya et al., Cancer Res. (2005) 65: 6071-6079 ( 2005)). Typically, these algorithms do not explicitly take into account contamination of tumor samples with benign tissue. See PCT / US2011 / 026098; Goransson et al., PLoS One (2009) 4 (6): e6057. This contamination is often high enough to make it difficult to detect the LOH region. Improved analytical methods according to the invention for identifying LOH, TAI and LST in the presence of contamination include those incorporated into computer software products such as:

The following is an example. If the observation ratio of the signals of the two alleles A and B is 2: 1, there are two possibilities. The first possibility is that in a sample contaminated with 50% normal cells, the cancer cells have an LOH with a deletion of allele B. The second possibility is that in a sample that is not contaminated with normal cells, LOH is absent but allele A is duplicated. Algorithms can be run as computer programs described herein to reconstruct the LOH region based on genotype (eg, SNP genotype) data. One of the key points of this algorithm is to first reconstruct the allele-specific copy count (ASCN) at each locus (eg, SNP). ASCN is the number of copies of both paternal and maternal alleles. The LOH region is subsequently determined as a series of SNPs in which one of the ASCNs (paternal or maternal) is 0. This algorithm can be based on maximizing the likelihood function and was previously described, designed to reconstruct the total number of copies (rather than ASCN) at each locus (eg, SNP). It may be conceptually similar to the algorithm. See International Application No. PCT / US2011 / 026098 for Abkevich et al. Likelihood functions can be maximized for ASCN at all loci, levels of benign tissue contamination, total number of copies averaged across the entire genome, and sample-specific noise levels. The input data to the algorithm was determined based on (1) sample-specific normalized signal intensity for both alleles at each locus, and (2) analysis of multiple samples with known ASCN profiles. It can or can consist of a set of specific parameters (specific for different SNP arrays and sequence-based approaches).

In some cases, nucleic acid sequencing techniques can be used to genotype loci. For example, genomic DNA from a cell sample (eg, a cancer cell sample) can be extracted and fragmented. For extraction and fragmentation of genomic nucleic acids, QIAamp ™ DNA Mini Kit (Qiagen ™), MagNA ™ Pure DNA Isolation Kit (Roche Applied Science ™) and GenElute ™ Mammalian Genomic DNA Miniprep Kit Any suitable method can be used, including but not limited to commercially available kits such as (Sigma-Aldrich ™). Once the extraction and fragmentation have taken place, either targeted sequencing or non-targeted sequencing can be used to genotype the sample at the locus. For example, whole-genome, whole transcriptome, or whole-exome sequencing can genotype millions or even billions of base pairs (ie, base pairs, It may be the "locus" to be evaluated).

In some cases, targeted sequencing of known polymorphic loci (eg, SNPs and surrounding sequences) can be performed as an alternative to microarray analysis. For example, loci for which genomic DNA is to be analyzed using kits designed for this purpose (eg, Agilent SureSelect ™, Illumina TruSeq Capture ™, and Nimblegen SeqCap EZ Choice ™). Fragments containing (eg, SNP position) can be concentrated. For example, genomic DNA containing the locus to be analyzed can be hybridized with a biotinylated capture RNA fragment to form a biotinylated RNA / genomic DNA complex. Alternatively, a DNA capture probe can be used to form a biotinylated DNA / genomic DNA hybrid. Magnetic beads and magnetic forces coated with streptavidin can be used to separate biotinylated RNA / genomic DNA complexes from genomic DNA fragments that are not present within the biotinylated RNA / genomic DNA complex. The resulting biotinylated RNA / genomic DNA complex can be processed to remove the captured RNA from the magnetic beads, thereby leaving intact genomic DNA fragments containing the loci to be analyzed. These intact genomic DNA fragments containing the loci to be analyzed can be amplified using, for example, PCR. Amplified genomic DNA fragments are high-throughput sequencing technologies such as Illumina HiSeq ™, Illumina MiSeq ™, Life Technologies SoLID ™ or Ion Torrent ™, or Roche 454 ™ or next-generation sequencing. Sequencing can be performed using singing techniques.

Similar to the microarray analysis described herein, sequencing results from genomic DNA fragments can be used to identify loci with or without CA. In some cases, the length of the CA region can be determined by genotyping a locus over a length of chromosome. For example, by sequencing a series of SNP positions located at intervals in the length direction of the chromosome (for example, at intervals of about 25 kb to about 100 kb), and using the sequencing results. , Not only the existence of the CA region existing in the length direction of the chromosome, but also the length of the CA region can be determined. Using the obtained sequencing results, it is possible to create a graph in which the amount of allele is plotted along the length direction of the chromosome. Allele amount d _i relates SNPi, can be calculated from the adjustment speed of the capture probe for the two alleles (A _i and _{B i): d i = A} i / (A i + B i). An example of such a graph is presented in FIGS. 1 and 2. Determining whether the abnormality is germline or somatic can be made as described herein.

In some cases, a selection process is used to evaluate loci using assays configured to genotype loci (eg, SNP array-based and sequencing-based assays). (For example, the SNP locus) can be selected. For example, any human SNP position can be selected for inclusion in an SNP array-based or sequencing-based assay configured to genotype a locus. In some cases, assessing SNP positions present in the human genome at 500,000, 1 million, 1.5 million, 2 million, 2.5 million or more, (a) not present on the Y chromosome, (b) not mitochondrial SNPs. , (C) have a minor allelic frequency of at least about 5% in Caucasians, (d) have a minor allelic frequency of at least about 1% in three non-white races (eg, Chinese, Japanese, and Yorba) SNPs can be identified that have and / or (e) do not significantly deviate from the Hardy-Weinberg equilibrium in any of the four races. In some cases, human SNPs above 100,000, above 150,000, or above 200,000 that meet the criteria (a) through (e) can be selected. Of the human SNPs that meet the criteria (a) to (e), SNPs have a high allelic frequency in whites and cover the human genome at somewhat uniform intervals (eg, every 25 kb to about 500 kb). The SNP group (eg, the top 110,000 SNPs) can be selected so that there is no linkage disequilibrium with another selected SNP in any of the four races (eg, at least one SNP). In some cases, select SNPs of approximately 40,000, 50,000, 60,000, 70,000, 80,000, 90,000, 100,000, 110,000, 120,000, 130,000 or more to meet these criteria. , Can be included in assays configured to identify CA regions throughout the human genome. For example, about 70,000 to about 90,000 (eg, about 80,000) SNPs can be selected for analysis using an SNP array-based assay. About 45,000 to about 55,000 (eg, about 54,000) SNPs can be selected for analysis using sequencing-based assays.

As described herein, any suitable type of sample can be evaluated. For example, evaluating a sample containing cancer cells, the cancer cell genome contains the HRD signature, lacks the HRD signature, has an increased number of indicator CA regions, or has an increased CA region score. It can be determined whether or not it is. Examples of samples containing cancer cells that can be evaluated as described herein include tumor biopsy samples (eg, breast tumor biopsy samples), formalin-fixed paraffin-embedded cancer cell-containing tissues. Includes, but is not limited to, a sample, a core needle biopsy sample, a fine needle aspirate, and a sample containing cancer cells shed from a tumor (eg, blood, urine, or other body fluid). For formalin-fixed, paraffin-embedded tissue samples, the samples are loaded into the kits described above (eg, QuickExtract ™ FFPE DNA Extraction Kit (Epicentre ™) and QIAamp ™ DNA FFPE Tissue Kit (Qiagen ™)). ), But can be prepared by DNA extraction using a genomic DNA extraction kit optimized for FFPE tissue.

In some cases, a laser dissection method can be performed on the tissue sample to minimize the number of non-cancer cells in the cancer cell sample to be evaluated. In some cases, antibody-based purification methods can be used to concentrate cancer cells and / or deplete non-cancer cells. Examples of antibodies that can be used for cancer cell enrichment include anti-EpCAM, anti-TROP-2, anti-c-Met, antifolate-binding protein, anti-N-cadherin, anti-CD318, anti-antimesencymal stem cells. Includes, but is not limited to, antigens, anti-Her2, anti-MUC1, anti-EGFR, anti-cytokeratin (eg, cytokeratin 7, cytokeratin 20, etc.), anti-caveolin-1, anti-PSA, anti-CA125, and anti-surfartinant protein antibodies. ..

Any type of cancer cell can be evaluated using the methods and materials described herein. For example, evaluate breast cancer cells, ovarian cancer cells, liver cancer cells, esophageal cancer cells, lung cancer cells, head and neck cancer cells, prostate cancer cells, colon cancer cells, rectal cancer cells, or colorectal cancer cells, and pancreatic cancer cells. To determine if the cancer cell genome contains the HRD signature, lacks the HRD signature, has an increased number of CA regions covering the entire chromosome, or has an increased CA region score. it can. In some embodiments, the cancer cell is a primary or metastatic cancer cell of ovarian cancer, breast cancer, lung cancer, or esophageal cancer.

When assessing the genome of a cancer cell for the presence or absence of an HRD signature, one or more pairs (eg, one pair, two pairs, three pairs, four pairs, five pairs, six pairs, seven pairs, eight). Pairs, 9 pairs, 10 pairs, 11 pairs, 12 pairs, 13 pairs, 14 pairs, 15 pairs, 16 pairs, 17 pairs, 18 pairs, 19 pairs, 20 pairs, 21 pairs, 22 pairs, or 23 pairs) Can be evaluated. In some cases, the genome of cancer cells may be divided into one or more pairs (eg, 1 pair, 2 pairs, 3 pairs, 4 pairs, 5 pairs, 6 pairs, 7 pairs, 8 pairs, 9 pairs, 10 pairs, 11 pairs). Presence or absence of HRD signature using chromosomes of pairs, 12 pairs, 13 pairs, 14 pairs, 15 pairs, 16 pairs, 17 pairs, 18 pairs, 19 pairs, 20 pairs, 21 pairs, 22 pairs, 23 pairs) To evaluate.

In some cases, it may be beneficial to exclude certain identified chromosomes from this analysis. For example, in the case of women, the pair to be evaluated may include an X sex chromosome pair; while in the case of men, any pair of autosomal chromosomes (ie, any pair other than the X and Y sex chromosome pairs). Pair) can be evaluated. As another example, in some cases, chromosome 17 pair may be excluded from the analysis. In certain cancers, certain chromosomes have been shown to have higher than normal levels of CA, and therefore these cancers when analyzing samples as described herein. It may be beneficial to exclude such chromosomes from patients with. In some cases, the sample is from a patient with ovarian cancer and the excluded chromosome is chromosome 17.

Therefore, a given number of chromosomes are analyzed to determine the number of indicator CA regions (or CA region score or composite CA region score), preferably above 9 megabases, above 10 megabases, above 12 megabases, 14 megabases. The total number of CA regions that exceed, more preferably exceed 15 megabases, may be determined. Alternatively or additionally, the size of all identified indicator CA regions can be summed to obtain the overall length of the indicator CA region.

As described herein, patients with cancer cells (or samples derived from them) identified as having an HRD signature condition will have a particular cancer, at least in part, based on such HRD signature condition. It can be categorized as likely to respond to a treatment regimen. For example, patients with cancer cells that have a genome with an HRD signature will have DNA damaging agents, synthetic lethal agents (eg, PARP inhibitors), radiation, or them, at least in part based on such HRD signature status. Can be classified as likely to respond to a cancer treatment regimen, including the use of a combination of. In some embodiments, the patient is an untreated patient. Examples of DNA damage agents include platinum-based chemotherapeutic agents (eg, cisplatin, carboplatin, oxaliplatin and picoplatin), anthracyclines (eg, epirubicin and doxorubicin), topoisomerase I inhibitors (eg, campothecin, topotecan and). Irinotecan), DNA cross-linking agents such as mitomycin C and triazene compounds (eg dacarbadin and temozolomide) are included, but not limited to. A therapeutic approach with synthetic lethality typically involves administering a drug that inhibits at least one critical component of a biological pathway that is particularly important for the survival of a particular tumor cell. For example, if the tumor cells have a deficiency in the homologous repair pathway (eg, as determined by the present invention), an inhibitor of the poly-ADP-ribose polymerase (or platinum-based drug, double-strand break repair inhibitor, etc.) May be particularly effective against such tumors, but this is because there are two pathways that are critical to survival (one biologically, eg, by BRCA1 mutation, the other). This is because it is blocked synthetically (eg, by administration of a pathway drug). Synthetic lethal approaches to cancer therapy are described, for example, in O'Brien et al., Converting cancer mutations into therapeutic opportunities, EMBO MOL. MED. (2009) 1: 297-299. Examples of synthetic lethal agents include, but are not limited to, PARP inhibitors or double-strand break repair inhibitors in homologous repair-deficient tumor cells, PARP inhibitors in PTEN-deficient tumor cells, methotrexate in MSH2-deficient tumor cells, and the like. .. Examples of PARP inhibitors include, but are not limited to, olaparib, iniparib, and veliparib. Examples of double-strand break repair inhibitors include, but are not limited to, KU55933 (ATM inhibitor) and NU7441 (DNA-PKcs inhibitor). Examples of information that can be used in addition to the presence of the HRD signature that underlies the classification of being more likely to respond to a particular cancer treatment regimen include previous treatment results, germline or somatic DNA suddenly. Mutation, gene or protein expression profiling (eg, ER / PR / HER2 status, PSA level), tumor histology (eg, adenocarcinoma, squamous epithelial cancer, serous papillary cancer, mucinous cancer, invasive ductal carcinoma, non-invasive ductal carcinoma Invasive ductal carcinoma (non-invasive), disease stage, tumor or cancer grade (eg, well-differentiated, moderately-differentiated, or poorly-differentiated (eg, Gleason, modified Bloom Richardson), etc.), of previous course of treatment The number of times etc. is included indefinitely.

Once classified as likely to respond to a particular cancer treatment regimen (eg, a cancer treatment regimen that includes the use of DNA damage agents, PARP inhibitors, radiation, or a combination thereof), cancer patients are such. It can be treated with a cancer treatment regimen. In some embodiments, the patient is an untreated patient. The present invention is therefore a method of treating a patient, comprising the step of detecting an HRD signature as described herein and the use of DNA damaging agents, PARP inhibitors, radiation, or a combination thereof. Provide methods that include the step of applying (or recommending or prescribing) a regimen. Any suitable method for treating the cancer in question can be used to treat cancer patients identified as having cancer cells with an HRD signature condition. For example, platinum-based chemotherapeutic agents or combinations of platinum-based chemotherapeutic agents can be used to treat cancer as described elsewhere (eg, U.S. Pat. Nos. 3,892,790, 3,904,663, 7,759,510, See Nos. 7,759,488 and 7,754,684). In some cases, anthracyclines or combinations of anthracyclines can be used to treat cancer as described elsewhere (eg, US Pat. Nos. 3,590,028, 4,138,480, 4,950,738, 6,087,340, See Nos. 7,868,040 and 7,485,707). In some cases, a combination of topoisomerase I inhibitors or topoisomerase I inhibitors can be used to treat cancer as described elsewhere (see, eg, US Pat. Nos. 5,633,016 and 6,403,563). In some cases, PARP inhibitors or combinations of PARP inhibitors can be used to treat cancer as described elsewhere (see, eg, US Pat. Nos. 5,177,075, 7,915,280, and 7,351,701). ). In some cases, radiation can be used to treat cancer as described elsewhere (see, eg, US Pat. No. 5,295,944). Combinations that include different agents (eg, platinum-based chemotherapeutic agents, anthracyclines, topoisomerase I inhibitors, and / or PARP inhibitors, with or without radiation therapy, as the case may be. ) Can be used to treat cancer. In some cases, combination therapy may be a combination of any of the above agents or treatments (eg, DNA damage agents, PARP inhibitors, radiation, or combinations thereof) with another drug or treatment, such as taxan agents (eg, doxetuximab). , Paclitaxel, Abraxane), growth factor inhibitors or growth factor receptor inhibitors (eg, erlotinib, gefitinib, lapatinib, sunitinib, bebasizumab, cetuximab, trussumab, panitumumab), and / or metabolic antagonists (eg, 5-fluorouracil (eg, 5-fluorouracil) It may be included together with flourouracil) and methotrexate).

In some cases, patients identified as having cancer cells with a genome lacking the HRD signature, at least partially based on a sample lacking the HRD signature, may receive DNA damage agents, PARP inhibitors, radiation, or a combination thereof. It can be categorized as less likely to respond to the treatment regimen that includes it. Subsequently, such patients are treated with one or more cancer treatments that are not associated with HDR, such as taxanes (eg, doxetuximab, paclitaxel, abraxane), growth factor inhibitors or growth factor receptor inhibitors (eg, eg). , Elrotinib, gefitinib, lapatinib, sunitinib, bebasizumab, cetuximab, trussutzumab, panitumumab), and / or likely to respond to cancer treatment regimens involving the use of antimetabolites (eg, 5-fluorouracil, methotrexate) Can be classified as. In some embodiments, the patient is an untreated patient. Treating a cancer patient with such a cancer treatment regimen once classified as likely to respond to a particular cancer treatment regimen (eg, a cancer treatment regimen that includes the use of cancer treatments that are not associated with HDR). Can be done. The present invention is therefore a method of treating a patient, the step of detecting the absence of an HRD signature as described herein, and the use of DNA damage agents, PARP inhibitors, radiation, or a combination thereof. Provide a method that includes the steps of giving (or recommending or prescribing) a treatment regimen that does not include it. In some embodiments, the therapeutic regimen includes taxanes (eg, doxetaxel, paclitaxel, abraxane), growth factor inhibitors or growth factor receptor inhibitors (eg, errotinib, gefitinib, lapatinib, sunitinib, bebashizumab, cetuximab, etc. Includes one or more of trastuzumab, panitumumab), and / or antimetabolites (eg, 5-fluorouracil, methotrexate). Any method appropriate for the cancer to be treated can be used to treat cancer patients identified as having cancer cells lacking the HRD signature. Examples of information that can be used in addition to the absence of the HRD signature that underlies the classification of being more likely to respond to a particular cancer treatment regimen include previous treatment results, germline or somatic DNA suddenly. Mutation, gene or protein expression profiling (eg, ER / PR / HER2 status, PSA level), tumor histology (eg, adenocarcinoma, squamous cell carcinoma, serous papillary carcinoma, mucinous cancer, invasive ductal carcinoma, non-invasive ductal carcinoma Invasive ductal carcinoma (non-invasive), disease stage, tumor or cancer grade (eg, well-differentiated, moderately-differentiated, or poorly-differentiated (eg, Gleason, modified Bloom Richardson), etc.), of previous course of treatment The number of times etc. is included indefinitely.

Once treated for a specific period of time (eg, 1-6 months), the patient can be evaluated to determine if the treatment regimen is effective. If a beneficial effect is detected, the patient can continue with the same or similar cancer treatment regimen. Adjustments can be made to the cancer treatment regimen if only minor beneficial effects are detected or no beneficial effects are detected. For example, the dose, frequency of administration, or duration of treatment can be increased. In some cases, additional anti-cancer agents may be added to the treatment regimen, or certain anti-cancer agents may be replaced with one or more different anti-cancer agents. Patients being treated can continue to be monitored as appropriate, and changes can be made to the cancer treatment regimen as appropriate.

In addition to predicting a likely therapeutic response or selecting the desired treatment regimen, the HRD signature can also be used to determine a patient's prognosis. Therefore, in one aspect, the document features a method for determining a patient's prognosis based, at least in part, on detecting the presence or absence of an HRD signature in a sample from a patient. The method determines whether (a) a sample from a patient contains cancer cells having the HRD signature described herein (sometimes referred to herein as having high HRD) ( Alternatively, the step of determining whether the sample contains DNA derived from such cells (eg, the presence of an indicator CA region or a higher CA region score or complex CA region score that exceeds the number of references), and ( b) (1) At least in the presence of an HRD signature or at least in the absence of a high HRD to determine that the patient has a relatively good prognosis, or (b) (2) in the absence of an HRD signature Partially, it includes or consists of steps in determining that the patient's prognosis is relatively poor. Prognosis may include the patient's chances of survival (eg, progression-free survival, overall survival), where a relatively good prognosis is for some reference population (eg, cancer type / subtype of this patient). It may include a higher chance of survival compared to the average patient with, the average patient without the HRD signature, etc.). Conversely, a prognosis that is relatively poor in terms of survival survives compared to some reference group (eg, the average patient with this patient's cancer type / subtype, the average patient with the HRD signature, etc.). It is thought that this includes the low probability of.

As described herein, this document provides a method for evaluating a patient for cells having a genome bearing the HRD signature (eg, cancer cells). In some embodiments, one or more clinicians or healthcare professionals determine whether a sample from a patient contains cancer cells bearing the HRD signature (or the sample contains DNA derived from such cells). Whether or not) can be determined. In some cases, one or more clinicians or healthcare professionals obtain a cancer cell sample from a patient, evaluate the cancer cell DNA of the cancer cell sample, and use the HRD signature as described herein. By determining the presence or absence, it can be determined whether the patient contains cancer cells bearing the HRD signature.

In some cases, one or more clinicians or healthcare professionals may obtain a cancer cell sample from a patient and provide the sample to a testing laboratory capable of evaluating the cancer cell DNA of the cancer cell sample. The presence or absence of the HRD signature as described herein can be indicated. In some embodiments, the patient is an untreated patient. In such cases, one or more clinicians or healthcare professionals receive information directly or indirectly from the laboratory about the presence or absence of the HRD signature so that the patient has cancer cells with the HRD signature. Whether it contains (or whether the sample contains DNA from such cells) can be determined. For example, a testing institution relates to a particular patient (or patient sample) to be evaluated by a clinician or healthcare professional after evaluating the DNA of a cancer cell for the presence or absence of an HRD signature as described herein. Written, electronic, or oral reports or medical records indicating the presence or absence of the HRD signature can be provided or made accessible. With such written, electronic or oral reports or medical records, one or more clinicians or healthcare professionals will find that the particular patient being evaluated contains cancer cells that carry the HRD signature. It can be determined whether or not.

Once a clinician or healthcare professional, or a group of clinicians or healthcare professionals, determines that a particular patient being evaluated contains cancer cells bearing the HRD signature, the clinician or healthcare professional (or group) , The patient can be classified as having cancer cells whose genome contains the presence of the HRD signature. In some embodiments, the patient is an untreated patient. In some cases, clinicians or healthcare professionals, or groups of clinicians or healthcare professionals, have HDR deficiencies in patients whose genome has been determined to have cancer cells that contain the presence of the HRD signature ( Or it can be diagnosed as having cancer cells (which are likely to be deficient). Such a diagnosis may simply be based on determining whether the sample from the patient contains cancer cells bearing the HRD signature (or whether the sample contains DNA derived from such cells). Alternatively, it may be at least partially based on determining whether a sample from a patient contains cancer cells bearing the HRD signature (or whether the sample contains DNA derived from such cells). For example, patients determined to have cancer cells with the HRD signature may be deficient in the HRD signature and one or more tumor suppressor genes (eg, BRCA1 / 2, RAD51C), a family history of cancer, or behavioral risk factors. Based on the combination of the presence of (eg, smoking), it can be diagnosed that HDR is likely to be deficient.

In some cases, a clinician or healthcare professional, or a group of clinicians or healthcare professionals, may have one or more patients in the HDR pathway whose genome has been determined to have cancer cells containing the presence of the HRD signature. It can be diagnosed as having cancer cells that are likely to contain a gene mutation in the gene of. In some embodiments, the patient is an untreated patient. Such a diagnosis may simply be based on the determination that the particular patient being evaluated has cancer cells with a genome containing the HRD signature, or the particular patient being evaluated has a genome containing the HRD signature. It may be at least partially based on the determination to have cancer cells with. For example, a patient whose genome is determined to have cancer cells containing the presence of an HRD signature will be based on a combination of the HRD signature and the presence of a family history of cancer, or the presence of behavioral risk factors (eg, smoking). It can be diagnosed as having cancer cells that are likely to contain a gene mutation in one or more genes in the HDR pathway.

In some cases, a clinician or healthcare professional, or a group of clinicians or healthcare professionals, will make a patient determined to have cancer cells with the HRD signature a cancer that is likely to respond to a particular cancer treatment regimen. It can be diagnosed as having cells. In some embodiments, the patient is an untreated patient. Such a diagnosis may simply be based on determining whether the sample from the patient contains cancer cells bearing the HRD signature (or whether the sample contains DNA derived from such cells). Alternatively, it may be at least partially based on determining whether a sample from a patient contains cancer cells bearing the HRD signature (or whether the sample contains DNA derived from such cells). For example, a patient determined to have cancer cells with an HRD signature may have a deficiency of the HRD signature and one or more tumor suppressor genes (eg, BRCA1 / 2, RAD51), a family history of cancer, or behavioral risk factors. Based on the combination of the presence of (eg, smoking), it can be diagnosed that it is likely to respond to a particular cancer treatment regimen. As described herein, patients determined to have cancer cells with the HRD signature are topotecanases such as platinum-based chemotherapeutic agents such as cisplatin, carboplatin, oxaliplatin or picoplatin, anthracyclines such as epirubicin or doxorubicin. Possibility to respond to a cancer treatment regimen that includes the use of I inhibitors, such as campothecin, topotecan or irinotecan, PARP inhibitors, radiation, combinations thereof, or a combination of any of the above with another anticancer drug. Can be diagnosed as high. In some embodiments, the patient is an untreated patient.

When a clinician or healthcare professional, or a group of clinicians or healthcare professionals, says that a sample from a patient contains cancer cells with a genome that lacks the HRD signature (or the sample contains DNA from such cells). Once determined, the clinician or healthcare professional (or group) can classify the patient as having cancer cells whose genome lacks the HRD signature. In some embodiments, the patient is an untreated patient. In some cases, clinicians or healthcare professionals, or groups of clinicians or healthcare professionals, are likely to have functional HDR in patients who are determined to have cancer cells that contain a genome that lacks the HRD signature. It can be diagnosed as having cancer cells. In some cases, a clinician or healthcare professional, or a group of clinicians or healthcare professionals, will send a patient determined to have cancer cells containing a genome that lacks the HRD signature to one or more genes in the HDR pathway. It can be diagnosed as having cancer cells that are unlikely to contain a gene mutation in. In some cases, a clinician or practitioner, or a group of clinicians or practitioners, may have cancer cells that contain a genome lacking the HRD signature or contain multiple CA regions that cover the entire chromosome. Platinum chemotherapeutic agents such as cisplatin, carboplatin, oxaliplatin or picoplatin, anthracyclines such as epirubicin or doxorubicin, topotecanase I inhibitors such as campothecin, topotecan or irinotecan, PARP inhibition Drugs or cancer therapeutics that are less likely to respond to radiation and / or are not HDR-related, such as one or more taxans, growth factor inhibitors or growth factor receptor inhibitors, antagonism It can be diagnosed as having cancer cells that are likely to respond to a cancer treatment regimen, including the use of agents and the like. In some embodiments, the patient is an untreated patient.

As described herein, this document also performs diagnostic analysis of nucleic acid samples from cancer patients (eg, genomic nucleic acid samples or genomic nucleic acid samples amplified from them), and samples from patients have HRD signatures and /. Alternatively, a method for determining whether or not a cancer cell containing a large number of CA regions covering the entire genome (or whether or not a sample contains DNA derived from such a cell) is provided. In some embodiments, the patient is an untreated patient. For example, one or more laboratory technicians or laborers may have the presence or absence of an HRD signature in the patient's cancer cell genome (or DNA derived from it), or a large number covering the entire chromosome in the patient's cancer cell genome. The presence or absence of the CA region can be detected. In some cases, one or more assay technicians or laborers either (a) receive a cancer cell sample from a patient or a genomic nucleic acid sample from a cancer cell obtained from a patient. Alternatively, receive such enriched and / or amplified genomic nucleic acid samples from cancer cells obtained from the patient and (b) analyze using the received material (eg, SNP array-based assay or sequencing). By performing a base assay) to detect the presence or absence of the HRD signature as described herein, or the presence or absence of multiple CA regions covering the entire chromosome, in the genome of the patient's cancer cells. The presence or absence of an HRD signature, or the presence or absence of multiple CA regions covering the entire genome can be detected. In some cases, one or more laboratory technicians or professionals may directly or indirectly from a clinician or healthcare professional sample to be analyzed (eg, a cancer cell sample obtained from a patient, from a patient A genomic nucleic acid sample obtained from the resulting cancer cells, or such enriched and / or amplified genomic nucleic acid samples obtained from cancer cells obtained from a patient) can be received. In some embodiments, the patient is an untreated patient.

Once an inspector or inspector, or a group of inspectors or inspectors, detects the presence of an HRD signature as described herein, the inspector or inspector (or group) will have that HRD signature. Alternatively, the results of a diagnostic analysis performed (or a summary of multiple results or results) can be associated with the corresponding patient's name, medical record, symbol / numeric identifier, or a combination thereof. Such identification may be based solely on detecting the presence of the HRD signature, or at least in part on detecting the presence of the HRD signature. For example, a laboratory technician or laboratory worker can determine a patient with cancer cells that has been detected to have the HRD signature, based on the combination of the HRD signature and the results of other genetic and biochemical tests performed at the laboratory. It can be identified as having cancer cells that are potentially HDR deficient (or likely to respond to a particular treatment as described in length herein). In some embodiments, the patient is an untreated patient.

The opposite of the above is also true. That is, once an inspector or inspector, or a group of inspectors or inspectors, detects the absence of an HRD signature, the inspector or inspector (or group) is responsible for the HRD signature or diagnostic analysis performed. Results (or multiple results or summaries of results) can be associated with the corresponding patient's name, medical record, symbol / numeric identifier, or a combination thereof. In some cases, a laboratory technician or laboratory worker, or a group of laboratory technicians or laboratory personnel, can treat patients with cancer cells detected to lack the HRD signature, either based solely on the absence of the HRD signature or of the HRD signature. Based on the combination of presence and the results of other genetic and biochemical tests performed in the laboratory, it has cancer cells with potentially intact HDR (or as described in length herein). Is unlikely to respond to a particular treatment). In some embodiments, the patient is an untreated patient.

The results of any analysis according to the invention can often be communicated to physicians, genetic counselors and / or patients (or other parties such as researchers) to any of the above parties or Communicated in a communicable form that can be communicated. Such shapes may vary and may or may not be touchable. The results can be embodied in descriptions, figures, photographs, charts, images, or any other visual form. For example, graphs or figures showing genotype or LOH (or HRD status) information can be used to illustrate the results. The description and visual form are of hand-touchable media such as paper, computer-readable media such as floppy disks, compact discs, flash memory, or non-touchable media such as e-mail. It can be recorded on electronic media in the form or on websites on the Internet or intranet. In addition, the results can be recorded in audio form and transmitted via any suitable medium, such as analog or digital cable lines, fiber optic cables, telephones, facsimiles, wireless mobile phones, internet telephones and the like.

Therefore, information and data about test results can be created anywhere in the world and communicated to different locations. As an exemplary example, when the assay is performed outside the United States, information and data about the test results are generated, cast in a communicable manner as described above, and then imported into the United States. To. Therefore, the invention also includes methods for generating communicable forms of information about the HRD signature for at least one patient sample. The method comprises (1) determining the HRD signature according to the method of the invention; and (2) communicatively embodying the results of the determining step. The transmissible form is the result of such a method.

Some aspects of the invention described herein include HRD signatures according to the invention (eg, total number of indicator CA regions above the number of references or CA region score or composite CA region score) and specific clinical. Features (eg, high probability of BRCA1 or BRCA2 gene deficiency; high probability of HDR deficiency; therapeutic regimen containing DNA damage agents, anthracyclines, topoisomerase I inhibitors, radiation, and / or PARP inhibitors, etc. It involves a step of correlating with (probability of response to) and optionally the absence of an HRD signature with one or more other clinical features. Wherever such aspects are described throughout this document, another aspect of the invention involves one or both of the following steps in addition to, or in place of, the correlating step: May be accompanied by: (a) at least partially based on the presence or absence of the HRD signature, to conclude that the patient has clinical features; or (b) at least partially based on the presence or absence of the HRD signature. The stage of communicating that the patient has clinical characteristics.

By way of example, but not limited to, one aspect described herein is the response of a cancer patient to a cancer treatment regimen that includes a DNA damaging agent, anthracycline, topoisomerase I inhibitor, radiation, and / or PARP inhibitor. (1) LOH region score for the sample; (b) TAI region score for the sample; or (c) two or more LST region scores for the sample. The steps to determine; and (2) (a) a combination of two or more of the LOH region score, TAI region score and LST region score above the reference count (eg, composite CA region score) in the treatment regimen. Steps to correlate with high likelihood of reaction; or optionally (2) (b) a combination of two or more of the LOH region score, TAI region score and LST region score not exceeding the number of references (eg, compound) The step of correlating the CA region score) with the low likelihood of responding to the treatment regimen; or optionally (2) (c) correlating the mean of the LOH region score, TAI region score and LST region score (eg, arithmetic mean). It is a method that includes the stage of attaching. According to the paragraph above, this description of this embodiment is construed to include a description of two related alternative modes. One such embodiment is a method of predicting the response of a cancer patient to a cancer treatment regimen that includes a DNA damaging agent, anthracycline, topoisomerase I inhibitor, radiation, and / or PARP inhibitor (1). In the sample, (a) LOH region score for the sample; (b) TAI region score for the sample; or (c) LST region score for the sample; or (d) mean of LOH region score, TAI region score and LST region score (eg) , Arithmetic average); and (2) (a) a combination of two or more of the LOH region score, TAI region score and LST region score that exceeds the number of references. The stage of concluding that the patient is likely to respond to the cancer treatment regimen, at least in part based on (eg, composite CA region score); or optionally (2) (b) the LOH region not exceeding the number of references. Score, a combination of two or more of the TAI region score and the LST region score (eg, composite CA region score), or at least the average of the LOH region score, TAI region score and LST region score (eg, arithmetic average) Provided is a method comprising, in part, concluding that the patient is unlikely to respond to the cancer treatment regimen. Another such embodiment is a method of predicting the response of a cancer patient to a cancer treatment regimen containing a DNA damaging agent, anthracycline, a topoisomerase I inhibitor, radiation, and / or a PARP inhibitor, (1) sample. In (a) LOH region score for the sample; (b) TAI region score for the sample; or (c) LST region score for the sample; or (d) the average of the LOH region score, TAI region score and LST region score (eg, The stage of determining two or more of the arithmetic mean); and (2) (a) a combination of two or more of the LOH region score, TAI region score and LST region score above the reference count. The patient is likely to respond to the cancer treatment regimen (eg, composite CA region score); or at least in part based on the average of the LOH region score, TAI region score, and LST region score (eg, arithmetic mean). The stage of communicating; or optionally (2) (b) a combination of two or more of the LOH region score, TAI region score and LST region score that does not exceed the number of references (eg, composite CA region score); Alternatively, a method comprising a step of communicating that the patient is unlikely to respond to the cancer treatment regimen, at least in part, based on the average of the LOH region score, TAI region score and LST region score (eg, arithmetic mean). provide.

The output of a particular assay or analysis (eg, the total number of indicator CA regions above the number of references, the presence of HRD signatures, etc.), some prospect of some clinical features (eg, response to a particular treatment, cancer-specific mortality, etc.) Correlate with (eg, increase, no increase, decrease, etc.), or additionally or alternatively, conclude such clinical features based at least in part on the output of such a particular assay or analysis. In each of the aspects described herein, with or with communication, such correlation, conclusion, or communication is a clinical feature, at least in part, based on the output of a particular assay or analysis. May include assigning a risk or likelihood of occurrence of. In some embodiments, such risk is the percent probability that an event or outcome will occur. In some embodiments, the patient is assigned to a risk group (eg, low risk, medium risk, high risk, etc.). In some embodiments, "low risk" is less than 5%, less than 10%, less than 15%, less than 20%, less than 25%, less than 30%, less than 35%, less than 40%, less than 45%, or 50. Any percentage probability less than%. In some embodiments, "medium risk" is above 5%, above 10%, above 15%, above 20%, above 25%, above 30%, above 35%, above 40%. Above, above 45%, or above 50%, and less than 15%, less than 20%, less than 25%, less than 30%, less than 35%, less than 40%, less than 45%, less than 50%, less than 55%, Any percentage probability of less than 60%, less than 65%, less than 70%, or less than 75%. In some embodiments, "high risk" is greater than 25%, greater than 30%, greater than 35%, greater than 40%, greater than 45%, greater than 50%, greater than 55%, greater than 60%. Any percentage probability above, above 65%, above 70%, above 75%, above 80%, above 85%, above 90%, above 95%, or above 99%.

As used herein, "transmitting" certain information means communicating such information to another person, or transferring such information to something (eg, a computer). Some methods of the invention convey the prognosis or prognosis of a patient in response to a particular treatment. In some embodiments, the information used to reach such predictions of prognosis or response (eg, HRD signatures according to the invention) is conveyed. This transmission may be auditory (eg, verbal), visual (eg, written), electronic (eg, data transferred from one computer system to another), and the like. In some embodiments, communicating a cancer classification (eg, prognosis, probable response, appropriate treatment, etc.) involves producing a report communicating the cancer classification. In some embodiments, the report is a paper report, an auditory report, or an electronic record. In some embodiments, the report is displayed and / or stored on a computer computer (eg, a handheld device, desktop computer, smart device, website, etc.). In some embodiments, the cancer classification is communicated to the physician (eg, a report communicating the classification is provided to the physician). In some embodiments, the cancer classification is communicated to the patient (eg, a report communicating the classification is provided to the patient). Cancer classification transfers information that embodies the classification (eg, data) to a server computer so that intermediate or end users can access such information (eg, when viewed from the server). By looking at the information, it can also be communicated (by downloading the information in the form of one or more files that are transferred from the server to intermediate or end user devices, etc.).

Whenever an aspect of the invention involves concluding any facts (eg, the prognosis of the patient, or the likelihood that the patient will respond to a particular treatment regimen), this typically, in some embodiments, will. After executing an algorithm that applies information about the CA domain in accordance with the present invention, it may include a computer program that concludes such facts.

Each aspect described herein involving several CA regions (eg, indicator CA regions), or the total length of such CA regions, or the average of composite CAR region scores (eg, arithmetic mean). In, the present invention is derived from such numbers or lengths, incorporates such numbers or lengths, and / or reflects such numbers or lengths to at least to some extent. Alternatively, the range includes related aspects involving scores (eg, CA region score, LOH region score, etc.). In other words, in various methods, systems, etc. of the present invention, the number or length of bare CA regions need not be used, and test values or scores derived from such numbers or lengths are used. You may use it. For example, one aspect of the invention is a method of treating cancer in a patient, wherein (1) the number of indicator LOH regions, (b) the number of indicator TAI regions, or (b) the number of indicator TAI regions in a sample from said patient. (C) Steps to determine two or more or averages (eg, arithmetic mean) of the number of indicator LST regions; (2) Derived from the number of indicator LOH regions, indicator TAI regions, and / or indicator LST regions. The step of providing one or more test values; (3) The test values are derived from the number of one or more reference values (eg, indicator LOH region, indicator TAI region, and / or indicator LST region in the reference population). Steps to compare with derived reference values (eg, mean, median, trisection, quadrant, quintuple, etc.); and (4) (a) one or more of the test values. Is greater than at least one of the above reference values (eg, at least 2x, 3x, 4x, 5x, 6x, 7x, 8x, 9x, or 10x; at least 1 standard deviation, 2 Standard deviation, 3 standard deviation, 4 standard deviation, 5 standard deviation, 6 standard deviation, 7 standard deviation, 8 standard deviation, 9 standard deviation, or 10 standard deviation larger) To administer an anticancer drug to the patient, or to recommend, prescribe, or initiate a treatment regimen containing chemotherapy and / or a synthetic lethal agent; or optionally (4). (B) One or more of the test values is not greater than at least one of the above reference values (eg, 2x, 3x, 4x, 5x, 6x, 7x, 8x, 9x or Not 10 times larger; 1 standard deviation, 2 standard deviation, 3 standard deviation, 4 standard deviation, 5 standard deviation, 6 standard deviation, 7 standard deviation, 8 standard deviation, 9 standard deviation, or 10 standard deviation not larger) Provided are methods that include a step of recommending, prescribing, or initiating a therapeutic regimen that does not include chemotherapy and / or synthetic lethal agents, at least in part, based on the comparative steps that make it clear. .. The present invention is modified as necessary to determine the patient's prognosis, the likelihood that the patient will respond to a particular treatment regimen, BRCA1 deficiency, BRCA2 deficiency, RAD51C deficiency, or HDR deficiency. Includes the corresponding aspects used to determine the likelihood that a patient's sample has.

FIG. 8 is an example in which a computer computing system (or a computer program (eg, software) containing computer executable instructions) can identify a LOH locus or region from genotype data as described herein. Shows the process. This process can be adapted for use in determining TAI and LST, as will be apparent to those of skill in the art. There are two possibilities when the observed ratio of the signals of the two alleles A and B is 2: 1. The first possibility is that the cancer cells have an allele B-deficient LOH in a sample that is 50% contaminated by normal cells. The second possibility is that allele A is duplicated in a sample that does not have LOH but is not contaminated with normal cells. The process starts in box 1500. In Box 1500, the following data: (1) sample-specific normalized signal intensity for both alleles at each locus and (2) assay defined based on analysis of multiple samples with known ASCN profiles. A specific set of parameters (specific for different SNP arrays and sequence-based approaches) is collected by the computer computing system. As described herein, any suitable assay, such as an SNP array-based assay or a sequencing-based assay, can be used to assess loci for homozygosity or heterozygosity along the chromosome. .. In some cases, using a system that includes a signal detector and a computer, data on homozygosity or heterozygotes of multiple loci (eg, fluorescent signals or sequencing results) (eg, for both alleles at each locus). Sample-specific normalized signal intensity) can be collected. In box 1510, the allele-specific copy count (ASCN) is reconstituted at each locus (eg, each SNP). ASCN is the number of copies of both paternal and maternal alleles. In Box 1530, a likelihood function is used to determine if the homozygous or homozygous locus region is due to LOH. This may be conceptually similar to the previously described algorithm designed to reconstruct the total number of copies (rather than ASCN) at each locus (eg, SNP). See International Application No. PCT / US2011 / 026098 to Abkevich et al. Likelihood functions can be maximized over ASCN at all loci, levels of contamination by benign tissues, total number of copies averaged across the entire genome, and sample-specific noise levels. In box 1540, the LOH region is determined as a series of SNPs in which one of the ASCNs (paternal or maternal) is 0. In some embodiments, the computer process further comprises inquiring if the patient is untreated, or determining if the patient is untreated.

Figure 3 shows an exemplary process by which a computer computing system can determine the presence or absence of a LOH signature, which, as will be apparent to those skilled in the art, how this process is TAI. And are included to illustrate if it can also be applied to LST. The process begins in Box 300, where data on homozygotes or heterozygotes of multiple loci along the chromosome is collected by a computer computing system. As described herein, any suitable assay, such as an SNP array-based assay or a sequencing-based assay, can be used to assess loci for homozygosity or heterozygosity along the chromosome. .. In some cases, a system equipped with a signal detector and a computer can be used to collect data on homozygosity or heterozygosity of multiple loci (eg, fluorescent signals or sequencing results). Box 310 evaluates the homozygous or heterozygous data of multiple loci as well as the position or spatial relationship of each locus by a computer computing system to determine the length of any LOH region along the chromosome. decide. In box 320, data on the number of detected LOH regions and the length of each detected LOH region is evaluated by a computer computing system and (a) longer than or greater than a preset Mb number (eg, 15 Mb), or Equal to this and (b) determine the number of LOH regions having a length shorter than the overall length of the chromosome containing the LOH region. Alternatively, the computer computing system can determine the overall length of the LOH as described above or determine the total length of the LOH. In box 330, the computer computing system formats the output indicating the presence or absence of the HRD signature. Once formatted, the computer computing system can present the output to the user (eg, a laboratory technician, clinician, or healthcare professional). As described herein, the presence or absence of an HRD signature is used to indicate a likely HDR status of a patient and to indicate a likely presence or absence of a gene mutation in a gene in the HDR pathway. , And / or possible cancer treatment regimens can be indicated.

FIG. 4 is an example of a computer device 1400 and a mobile computer device 1450 that can be used with the techniques described herein. The computer computer 1400 is intended to be various types of digital computers, such as laptops, desktops, workstations, personal digital assistants, servers, blade servers, mainframes, and other suitable computers. Computer computing device 1450 is intended to be various types of mobile devices, such as personal digital assistants, mobile phones, smartphones, and other similar computer computing devices. The components shown herein, their connections and relationships, and their functions are intended to be illustrative only and are not intended to limit the practice of the invention described and / or claimed herein.

The computer computer 1400 comprises a processor 1402, a memory 1404, a storage device 1406, a high-speed interface 1408 connected to the memory 1404 and the high-speed expansion port 1410, and a low-speed interface 1415 connected to the low-speed bus 1414 and the storage device 1406. .. The components 1402, 1404, 1406, 1408, 1410, and 1415 are each interconnected using various buses and may be mounted on a common motherboard or in other ways as appropriate. Processor 1402 is a computer computing device that includes instructions stored in memory 1404 or storage 1406 to display graphical information for a GUI on an external input / output device, eg, display 1416 connected to high speed interface 1408. Can handle instructions to execute in the 1400. In other executions, multiple processors and / or multiple buses may be used, as appropriate, with multiple memory and memory types. Also, multiple computer computing devices 1400 may be connected, and each device provides some of the required operations (eg, as a server bank, a collection of blade servers, or a multiprocessor system).

The memory 1404 stores information in the computer computer 1400. In one run, memory 1404 is a volatile memory unit. In another run, memory 1404 is a non-volatile memory unit. Memory 1404 may also be another type of computer-readable medium, such as a magnetic disk or optical disk.

The storage device 1406 can provide a large amount of storage to the computer computing device 1400. In one run, the storage device 1406 is a computer-readable medium, such as a floppy disk device, a hard disk device, an optical device, or a tape device, a flash memory or other similar solid state memory device, or in a storage area network or other. It may be a number of different devices, including the devices being configured, and may be equipped with these. Computer program products can be incorporated into information carriers so that they can be touched. Computer program products may also include instructions that, when executed, perform one or more methods, eg, the methods described herein. The information carrier is a computer-readable or machine-readable medium, such as memory 1404, storage 1406, memory mounted on processor 1402, or propagating signal.

The high-speed controller 1408 manages bandwidth-intensive operations for the computer computer 1400, while the low-speed controller 1415 manages low-bandwidth-intensive operations. The assignment of such functions is only an example. In one run, the fast controller 1408 is connected to memory 1404, display 1416 (eg, via a graphics processor or accelerator), and fast expansion port 1410, which fast expansion port 1410 connects to various expansion cards (not shown). You may accept it. In this run, the slow controller 1415 is connected to storage 1406 and slow expansion port 1414. The slow expansion port may have a variety of communication ports (eg USB, Bluetooth, Ethernet, or Wireless Ethernet), eg, via a network adapter, one or more input / output devices, eg a keyboard. , Pointing devices, scanners, optical readers, fluorescent signal detectors, or networking devices, such as switches or routers.

As shown in the drawing, the computer computer 1400 can be executed in many different forms. For example, computer computer 1400 may be run as a standard server 1420, or may be run multiple times in such a collection of servers. Computer computer 1400 may be run as part of rack server system 1424. In addition, computer computer 1400 may be run in a personal computer, such as laptop computer 1422. Alternatively, components from computer computing device 1400 may be combined with other components in the mobile device (not shown), such as device 1450. Such a device may include one or more of computer computing devices 1400, 1450, respectively, and the entire system may consist of a plurality of computer computing devices 1400, 1450 communicating with each other.

The computer computer 1450 includes a processor 1452, a memory 1464, an input / output device such as a display 1454, a communication interface 1466, and a transceiver 1468 among its components (eg, scanner, optical reader, fluorescent signal detector). .. Device 1450 may also be provided with a storage device such as a microdrive or other device to provide additional storage. The components 1450, 1452, 1464, 1454, 1466, and 1468 are each interconnected using different buses, and some of the components may be mounted on a common motherboard or in other ways as appropriate.

Processor 1452 can execute instructions in computer computer 1450, including instructions stored in memory 1464. The processor may be run as a chipset of chips with separate and multiple analog and digital processors. The processor may provide, for example, control of the user interface, applications driven by the device 1450, and wireless communication by the device 1450 in order to successfully coordinate other components of the device 1450.

Processor 1452 can communicate with the user via display interface 1456 connected to control interface 1458 and display 1454. The display 1454 may be, for example, a TFT LCD (thin film transistor liquid crystal display) or OLED (organic light emitting diode) display or other suitable display technology. The display interface 1456 may include suitable circuitry for driving the display 1454 to present graphic and other information to the user. Control interface 1458 may receive commands from the user and translate the commands for transmission to processor 1452. In addition, the external interface 1462 may communicate with the processor 1452 to allow near area communication between device 1450 and other devices. The external interface 1462 may, for example, provide wired communication in some executions, wireless communication in other executions, and may use multiple interfaces.

The memory 1464 stores information in the computer computer 1450. Memory 1464 can be run as one or more of a computer-readable medium, a volatile memory unit, or a non-volatile memory unit. Extended memory 1474 may be installed via extended interface 1472 and connected to device 1450. The expansion interface 1472 may include, for example, a SIMM (single inline memory module) card interface. Such extended memory 1474 may provide extra storage space to device 1450 and may store applications or other information for device 1450. For example, extended memory 1474 may include instructions that perform or supplement the processes described herein, and may also include secure information. Thus, for example, the extended memory 1474 may be provided as a security module for the device 1450 or may be programmed with instructions that allow the safe use of the device 1450. In addition, secure applications may be provided with additional information via the SIMM card, such as inserting identification information into the SIMM card to prevent hacking.

The memory may include, for example, flash memory and / or NVRAM memory as discussed below. In one run, the computer program product is incorporated into the information carrier so that it can be touched. Computer program products include instructions that, when executed, perform one or more methods, eg, the methods described herein. The information carrier is a computer-readable or machine-readable medium, such as memory 1464, extended memory 1474, memory mounted on processor 1452, or a propagating signal that can be received, such as a propagating signal that can be received on a transceiver 1468 or an external interface 1462. Is.

The device 1450 may wirelessly communicate via the communication interface 1466. Communication interface 1466 may include a digital signal processing circuit, if desired. Communication interface 1466 may provide communication under various modes or protocols, such as GSM voice call, SMS, EMS, or MMS messaging, CDMA, TDMA, PDC, WCDMA, CDMA2000, or GPRS. Such communication may occur, for example, via the radio frequency transceiver 1468. In addition, short-range communications may occur using, for example, Bluetooth, WiFi, or other such transceivers (not shown). In addition, the GPS (Global Positioning System) receiver module 1470 may provide additional navigation-related radio data and location-related radio data to device 1450, and navigation-related radio data and position-related radio data may be provided on device 1450 as appropriate. It may be used by an application running on.

The device 1450 may also use the audio codec 1460 for audible sound communication. The audio codec 1460 can receive voice information from the user and convert it into usable digital information. In addition, the audio codec 1460 can generate audible sounds to the user, for example, through speakers, for example, in the handset of device 1450. Such voice may include sound from a voice telephone call, may include recorded voice (eg, voice mail, music files, etc.), or may also include voice created by an application running on the device 1450. ..

As shown in the drawings, the computer computer 1450 can be implemented in a number of different forms. For example, the computer computer 1450 may be executed as a mobile phone 1480. Computer computing device 1450 may also be run as part of a smartphone 1482, personal digital assistant, or other similar mobile device.

The various implementations of the systems and techniques described herein include digital electronic circuits, integrated circuits, specially designed ASICs (application specific integrated circuits), computer hardware, firmware, software, and / or combinations thereof. Can be realized in. These various executions receive data and instructions from the storage system, at least one input device, and at least one output device, and send data and instructions to the storage system, at least one input device, and at least one output device. Includes execution in one or more computer programs runnable and / or interpretable on a programmable system, including at least one programmable processor, which may be special or general purpose, connected to transmit. Good.

These computer programs (also known as programs, software, software applications, or code) include programmable processor machine instructions and run in high-level procedural and / or object-oriented programming languages and / or assembly / machine languages. can do. As used herein, the terms "machine-readable medium" and "computer-readable medium" are optional used to provide machine instructions and / or data to a programmable processor that includes a machine-readable medium that receives machine instructions as a machine-readable signal. Computer program products, equipment, and / or equipment (eg, magnetic disks, optical disks, memory, and programmable logical devices (PLDs)). The term "machine readable signal" refers to any signal used to provide machine instructions and / or data to a programmable processor.

The systems and techniques described herein to provide user interaction include display devices (eg, CRT (cathode line tube) or LCD (liquid crystal display) monitors) for displaying information to the user and the user computer. It can be run on a computer that has a keyboard and pointing device (eg, a mouse or trackball) that allows you to type in. Other types of devices can also be used to provide dialogue with the user. For example, the feedback provided to the user may be any type of sensory feedback (eg, visual feedback, auditory feedback, or tactile feedback). Inputs from the user can be received in any form, including acoustic input, voice input, or tactile input.

The systems and techniques described herein include back-end components (eg, as data servers), or middleware components (eg, application servers), or front-end components (eg, users, for example. A client computer with a graphical user interface or web browser to be able to interact with the performance of the systems and techniques described in the document), or any combination of such back-end, middleware, or front-end components. It can be executed in a computer computing system provided. The components of the system can be interconnected by any form or medium of digital data communication (eg, a communication network). Examples of communication networks include local area networks (“LAN”), wide area networks (“WAN”), and the Internet.

The computer computing system may include clients and servers. Clients and servers are generally separated from each other and typically interact over a communication network. The client-server relationship is generated by computer programs that run on their respective computers and have a client-server relationship with each other.

In some cases, the computer computing system provided herein may be configured to include one or more sample analyzers. The sample analyzer may be configured to generate multiple signals for at least a pair of human chromosomal genomic DNAs from cancer cells. For example, a sample analyzer can generate a signal that can be interpreted in a way that identifies homozygotes or heterozygotes of loci along the chromosome. In some cases, the sample analyzer may be configured to perform one or more stages of an SNP array-based assay or a sequencing-based assay, generating and / or capturing signals from such assays. It may be configured to do so. In some cases, the computer computing system provided herein may be configured to include a computer computing device. In such cases, the computer computer may be configured to receive a signal from the sample analyzer. The computer computing device may include computer-executable instructions or computer programs (eg, software) that include computer-executable instructions for performing one or more of the methods or steps described herein. In some cases, such computer-executable instructions direct the computer computer to analyze signals from a sample analyzer, another computer computer, an SNP array-based assay, or a sequencing-based assay. Can be done. Analyzing such signals to determine genotype, homozygosity or other chromosomal aberrations at a particular locus, CA region, number of CA regions, size of CA region, specific Determining the number of CA regions with size or size range, determining if a sample is HRD signature positive, determining the number of indicator CA regions in at least one pair of human chromosomes, the BRCA1 gene and / Or determine the likelihood of BRCA2 gene deficiency, determine the likelihood of HDR deficiency, cancer patients with certain cancer treatment regimens (eg, DNA damage agents, anthracyclins, topoisomerase I inhibitors, radiation, PARP It is possible to determine the likelihood of responding to an inhibitor (or a regimen containing a combination thereof), or to determine a combination of these items.

In some cases, the computer computing system provided herein is the number of CA regions, the size of the CA regions, the number of CA regions with a particular size or size range, and whether the sample is positive for the HRD signature. , Number of indicator CA regions in at least one pair of human chromosomes, BRCA1 and / or BRCA2 gene deficiency probabilities, HDR deficiency probable determination, cancer patients specific cancer treatment regimens (eg, DNA damage agents, anthra) A computer-executable instruction or computer for formatting output that is likely to respond to cyclins, topoisomerase I inhibitors, radiation, PARP inhibitors, or a regimen containing a combination thereof) or provides an indicator of a combination of these items. It may include a computer program (eg, software) that includes executable instructions. In some cases, the computer computing system provided herein is for determining the preferred cancer treatment regimen for a particular patient, at least in part, based on the presence or absence of an HRD signature, or the number of indicator CA regions. , Computer executable instructions or computer programs (eg, software) that include computer executable instructions.

In some cases, the computer computing systems provided herein are configured to process samples (eg, cancer cells) so that SNP array-based or sequencing-based assays can be performed. A pretreatment device may be provided. Examples of pretreatment devices include devices configured to concentrate cell populations on cancer cells as opposed to non-cancer cells, devices configured to lyse cells and / or extract genomic nucleic acids. , As well as, but are not limited to, devices configured to concentrate samples for specific genomic DNA fragments.

The document also provides a kit for evaluating samples (eg, cancer cells) as described herein. For example, this document provides a kit for assessing cancer cells for the presence of the HRD signature, or for determining the number of indicator CA regions in at least one pair of human chromosomes. The kits provided herein are SNP probes (eg, arrays of SNP probes for performing SNP array-based assays described herein) or primers (eg, SNPs via sequencing-based assays). A computer-executable instruction (eg, a particular size or size range) for performing one or more of the methods or steps described herein with any of the primers (primers designed to sequence regions). It may be included in combination with a computer program product that includes computer executable instructions) to determine the number of CA regions it has. In some cases, the kits provided herein may include at least 500, 1000, 10,000, 25,000, or 50,000 SNP probes capable of hybridizing to polymorphic regions of human genomic DNA. .. In some cases, the kits provided herein may contain at least 500, 1000, 10,000, 25,000, or 50,000 primers capable of sequencing polymorphic regions of human genomic DNA. In some cases, the kits provided herein may include one or more other components for performing SNP array-based assays or sequencing-based assays. Examples of such other components include, but are not limited to, buffers, sequencing nucleotides, enzymes (eg, polymerases), and the like. This document also provides the use of any suitable number of materials provided herein in the manufacture of a kit for performing one or more of the methods or steps described herein. For example, this document is provided herein with a collection of SNP probes (eg, a collection of 10,000 to 100,000 SNP probes) in the manufacture of kits for assessing cancer cells for the presence of HRD signatures. Provide use of computer program products. As another example, this document describes a collection of primers (eg, a collection of 10,000 to 100,000 primers for sequencing SNP regions) in the manufacture of kits for assessing cancer cells for the presence of HRD signatures. ) And the use of the computer program products provided herein.

Specific Aspects The following are exemplary, but not limited, details of the specific aspects of the present disclosure, i.e., the methods and systems according to the more general description above.

In some embodiments, the sample used is a frozen tumor sample. In some embodiments, the sample is derived from a particular breast cancer subtype selected from triple negative, ER + / HER2-, ER- / HER2 +, or ER + / HER2 +. In some embodiments, the testing assay portion of the method, system, etc. comprises assaying the sample to perform sequencing of the BRCA1 and / or BRCA2 gene (and any other one or more in Table 1). Gene). In some embodiments, testing assay parts such as methods, systems, etc. are allergens for selected SNPs of at least 10,000, 20,000, 30,000, 40,000, 50,000, 60,000, 70,000, 80,000, 90,000, 100,000 or more throughout the genome Includes assaying samples to determine (eg, genotype, number of copies, etc.). In some embodiments, SNP analysis is performed using oligonucleotide microarrays as discussed above. In some embodiments, BRCA sequence analysis, SNP analysis, or both, probe capture (eg, a probe for each SNP to be analyzed, and / or a probe for capturing the entire coding region of BRCA1 and / or BRCA2. ), Followed by a PCR enrichment technique (eg, Agilent ™ SureSelect XT). In some embodiments, BRCA sequence analysis, SNP analysis, or both are performed by processing the output by the enrichment technique using a "next generation" sequencing platform (eg, Illumina ™ HiSeq2500). In some embodiments, the sample is analyzed for somatic and / or germline mutations in BRCA1 / 2, which may involve large-scale rearrangements. In some embodiments, the sample is analyzed for methylation of the BRCA1 promoter (eg, by qPCR assay (eg, SA Biosciences)). In some embodiments, the sample is greater than 10% (or 5%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%) methylated (eg, BRCA1 or BRCA2). If it has (percentage of methylation of the promoter CpG) of the sample, it is determined that the sample has (or is "methylated") highly methylated. In some embodiments, from the patient's matched normal (non-tumor) tissue, for example, to determine whether the BRCA1 or BRCA2 mutation is germline or somatic. DNA may be analyzed.

In some embodiments, the LOH region score can be calculated by calculating the number of LOH regions that are greater than 15 Mb in length but shorter than the length of the entire chromosome. In some embodiments, the TAI region score can be calculated by calculating the number of telomere regions with an allelic imbalance that is greater than 11 Mb in length and extends to one of the subtelomeres but does not exceed the centromere. In some embodiments, the LST region score is calculated by screening out regions shorter than 3 megabases and then calculating the number of discontinuities between regions longer than 10 megabases with stable copy numbers. be able to. In some embodiments, the LST region score can be modified by adjusting for ploidy: LSTm = LST-kP, in the equation, P is ploidy and k is a constant (some embodiments). In, k = 15.5). In some embodiments, BRCA1 / 2 deficiency can be defined as loss of function due to mutations in BRCA1 or BRCA2, or methylation of the promoter region of BRCA1 or BRCA2, with LOH in the affected gene. .. In some embodiments, the response to treatment may be a partial complete response (“pCR”), which in some embodiments is defined as the condition of Miller-Payne 5 after treatment (eg, neoadjuvant). be able to.

In some embodiments, the claimed method is to ^{eliminate BRCA defects at least 8 *} 10 ^-12 , 6 ^* 10 ^-6 , 0.0009, 0.01, 0.03, 2 ^* 10 ^-16 , 3 ^* 10 ^-6 , 10 ^-6. , 0.0009, 8 ^* 10 ^-12 , 2 ^* 10 ^-16 , 8 ^* 10 ^-8 , 6 ^* 10 ^-6 , 3 ^* 10 ^-6 or 0.0002 p-values (for example, these p-values are obtained) Each CA area score is predetermined and multiple scores are optionally combined). In some embodiments, the p-value is calculated by the Kolmogorov-Smirnov test. In some embodiments, the HRD score and age at diagnosis can be encoded as a numerical (eg, integer) variable, the breast cancer stage and subtype can be encoded as a categorical variable, and the grade can be a numerical variable or It can be analyzed as either or both of the categorical variables.

In some embodiments, the p-value is bilateral. In some embodiments, logistic regression analysis can be used to predict BRCA1 / 2 deficiency based on HRD scores, including HRD-composite scores, as disclosed herein. In some embodiments, the various CA region scores are correlated according to the following correlation coefficients (eg, defined for the purpose of achieving:): LOH region score and TAI region score = 0.69 (p = 10). ^-39 ), between LOH and LST = 0.55 (p = 2 ^* 10 ^-19 ) and between TAI and LST = 0.39 (p = 10 ^-9 ).

In some embodiments, the method has a LOH region score and a TAI region score to detect a BRCA1 / 2 deficiency and / or to predict a therapeutic response (eg, response to platinum therapy (eg, cisplatin)). Are combined as follows: Composite CA area score = 0.32 ^* LOH area score + 0.68 ^* TAI area score. In some embodiments, the method has a LOH region score, a TAI region score, to detect a BRCA1 / 2 deficiency and / or to predict a therapeutic response (eg, response to platinum therapy (eg, cisplatin)). And the LST region score are combined as follows: Composite CA region score = 0.21 ^* LOH region score + 0.67 ^* TAI region score ^{+ 0.12 *} LST region score. In some embodiments, the method has a LOH region score, a TAI region score, to detect a BRCA1 / 2 deficiency and / or to predict a therapeutic response (eg, response to platinum therapy (eg, cisplatin)). And the LST region score are combined as follows: Composite CA region score = 0.1 1 ^* LOH region score + 0.25 ^* TAI region score ^{+ 0.12 *} LST region score. In some embodiments, the method has a LOH region score, a TAI region score, to detect a BRCA1 / 2 deficiency and / or to predict a therapeutic response (eg, a response to platinum therapy (eg, cisplatin)). And the LST region score are combined as follows: Composite CA region score = LOH region score, TAI region score and arithmetic mean of the LST region score.

In some embodiments, the combination of BRCA-deficient and HRD states can predict therapeutic response. For example, the present disclosure presents a patient (eg, for example) for a cancer treatment regimen that includes a DNA damaging agent (eg, a platinum agent, such as cisplatin), anthracyclines, topoisomerase I inhibitors, radiation, and / or PARP inhibitors. , A method of predicting the response of triple-negative breast cancer patients)
In a cancer cell derived from a patient sample, the number of indicator CA regions (eg, indicator LOH region, indicator TAI region, indicator LST region, or any combination thereof) in at least one pair of human chromosomes of the cancer patient's cancer cells. Stage to decide;
The step of determining whether cancer cells from a patient sample have BRCA1 or BRCA2 deficiency (eg, deleterious mutations, high promoter methylation); and the sample is (a) the number of said indicator CA regions. Patients with greater than the number of references, or (b) either BRCA1 or BRCA2 deficient, or both (a) and (b) are diagnosed as likely to respond to the cancer treatment regimen. stage,
Can include methods including.

Further Specific Aspects Aspects 1. An in vitro method that predicts patient response to a cancer treatment regimen that includes DNA damage agents, anthracyclines, topoisomerase I inhibitors, or PARP inhibitors.
(1) In a sample containing cancer cells, the number of indicator CA regions containing at least two types selected from the indicator LOH region, the indicator TAI region, or the indicator LST region in at least one pair of human chromosomes of the cancer cells of a cancer patient. And (2) the step of diagnosing a patient whose sample has more indicator LOH, indicator TAI, or indicator LST regions than the reference number is likely to respond to the cancer treatment regimen. Including, method.

Aspect 2. The method of aspect 1, wherein at least one pair of human chromosomes represents the entire genome.

Aspect 3. Indicator CA regions are at least 2 pairs, 3 pairs, 4 pairs, 5 pairs, 6 pairs, 7 pairs, 8 pairs, 9 pairs, 10 pairs, 11 pairs, 12 pairs, 13 pairs, 14 pairs, 15 pairs, 16 pairs, The method of aspect 1 or aspect 2, as determined on 17 pairs, 18 pairs, 19 pairs, 20 pairs or 21 pairs of human chromosomes.

Aspect 4. The method according to any one of aspects 1 to 3, wherein the cancer cell is an ovarian cancer cell, a breast cancer cell, or an esophageal cancer cell.

Aspect 5. The number of references in the indicator LOH area is 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23. , 24, 25, 30, 35, 40, 45, 50 or more, and the number of references in the indicator TAI region is 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 , 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50 or better, and reference to the indicator LST region. Numbers are 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 40 45, 50, or more, the method according to any of aspects 1-4.

Aspect 6. Indicator LOH region has a length of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22 , 23, 24, 25, 30, 35, 40, 45, 50 Megabase or greater, but defined as the LOH region shorter than either the complete chromosome or the complete chromosome arm, the indicator TAI region is longer At least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 , 30, 35, 40, 45, 50 Megabase or greater, but defined as the TAI region that does not extend beyond the centromere, and the indicator LST region is at least 2, 3, 4, 5, in length. 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50 megabase The method according to any of aspects 1-5, which is defined as an LST region that is or exceeds.

Aspect 7. DNA damage agents are cisplatin, carboplatin, oxalaplatin or picoplatin, anthracyclines are epirubincin or doxorubicin, and topoisomerase I inhibitors are campothecin, topotecan or irinotecan, or PARP inhibitors. The method according to any of aspects 1-6, wherein is iniparib, olaparib or velapirib.

Aspect 8. The method of any of aspects 1-7, further comprising the step of administering a cancer treatment regimen to a patient diagnosed with a high likelihood of responding to the cancer treatment regimen.

Aspect 9. An in vitro method that predicts patient response to a cancer treatment regimen that includes a platinum agent.
(1) In a sample containing cancer cells, the number of indicator CA regions containing at least two types selected from the indicator LOH region, the indicator TAI region, or the indicator LST region in at least one pair of human chromosomes of the cancer cells of a cancer patient. Stage to decide;
(2) The stage of determining whether a sample containing cancer cells is deficient in BRCA1 or BRCA2; and (3) in that sample, (a) the number of indicator LOH regions, indicator TAI regions, or indicator LST regions Patients who are larger than the number of references, or (b) deficient in BRCA1 or BRCA2, or either (a) or (b) are diagnosed as likely to respond to the cancer treatment regimen. A method, including steps.

Aspect 10. The method of aspect 9, wherein at least one pair of human chromosomes represents the entire genome.

Aspect 11. Indicator CA regions are at least 2 pairs, 3 pairs, 4 pairs, 5 pairs, 6 pairs, 7 pairs, 8 pairs, 9 pairs, 10 pairs, 11 pairs, 12 pairs, 13 pairs, 14 pairs, 15 pairs, 16 pairs, 9. The method of aspect 9 or 10, as determined on 17 pairs, 18 pairs, 19 pairs, 20 pairs or 21 pairs of human chromosomes.

Aspect 12. The method according to any of aspects 9-11, wherein the cancer cells are ovarian cancer cells, breast cancer cells, or esophageal cancer cells.

Aspect 13. The number of references in the indicator LOH area is 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23. , 24, 25, 30, 35, 40, 45, 50 or more, and the number of references in the indicator TAI region is 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 , 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50 or better, and reference to the indicator LST region. Numbers are 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50, or more, the method according to any of aspects 9-12.

Aspect 14. Indicator LOH region has a length of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22 , 23, 24, 25, 30, 35, 40, 45, 50 Megabase or greater, but defined as the LOH region shorter than either the complete chromosome or the complete chromosome arm, the indicator TAI region is longer At least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 , 30, 35, 40, 45, 50 Megabase or greater, but defined as the TAI region that does not extend beyond the centromere, and the indicator LST region is at least 2, 3, 4, 5, in length. 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50 megabase The method according to any of aspects 9-13, which is defined as an LST region that is or exceeds.

Aspect 15. DNA damage agents are cisplatin, carboplatin, oxalaplatin or picoplatin, anthracyclines are epirubincin or doxorubicin, and topoisomerase I inhibitors are campothecin, topotecan or irinotecan, or PARP inhibitors. The method according to any of aspects 9-14, wherein is iniparib, olaparib or velapirib.

Aspect 16. Described in any of aspects 9-15, wherein the sample is deficient in BRCA1 or BRCA2 if a mutation, heterozygosity loss or high methylation that is harmful to either BRCA1 or BRCA2 is detected in the sample. the method of.

Aspect 17. Methylation is at least 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, or 50% of the analyzed BRCA1 or BRCA2 promoter CpG, or better. 16. The method of aspect 16, wherein highly methylation is detected when detected.

Aspect 18. An in vitro method that predicts patient response to a cancer treatment regimen that includes DNA damage agents, anthracyclines, topoisomerase I inhibitors, or PARP inhibitors.
(1) In a sample containing cancer cells, the number of indicator CA regions containing at least two types selected from the indicator LOH region, the indicator TAI region, or the indicator LST region in at least one pair of human chromosomes of the cancer cells of a cancer patient. Stage to decide;
(2) The stage of providing a test value derived from the number of the indicator CA regions;
(3) The step of comparing the test value to one or more reference values derived from the number of the indicator CA regions in the reference population; and (4) the test value is the one or more references in the sample. A method comprising diagnosing a larger number of patients as likely to respond to the cancer treatment regimen.

Aspect 19. The method of aspect 18, wherein at least one pair of human chromosomes represents the entire genome.

Aspect 20. Indicator CA regions are at least 2 pairs, 3 pairs, 4 pairs, 5 pairs, 6 pairs, 7 pairs, 8 pairs, 9 pairs, 10 pairs, 11 pairs, 12 pairs, 13 pairs, 14 pairs, 15 pairs, 16 pairs, The method of aspect 18 or aspect 19, as determined on 17 pairs, 18 pairs, 19 pairs, 20 pairs or 21 pairs of human chromosomes.

Aspect 21. The method according to any of aspects 18-20, wherein the cancer cells are ovarian cancer cells, breast cancer cells, or esophageal cancer cells.

Aspect 22. The number of references in the indicator LOH area is 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23. , 24, 25, 30, 35, 40, 45, 50 or more, and the number of references in the indicator TAI region is 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 , 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50 or better, and reference to the indicator LST region. Numbers are 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50, or more, the method according to any of aspects 18-21.

Aspect 23. Indicator LOH region has a length of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22 , 23, 24, 25, 30, 35, 40, 45, 50 Megabase or greater, but defined as the LOH region shorter than either the complete chromosome or the complete chromosome arm, the indicator TAI region is longer At least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 , 30, 35, 40, 45, 50 Megabase or greater, but defined as the TAI region that does not extend beyond the centromere, and the indicator LST region is at least 2, 3, 4, 5, in length. 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50 megabase The method according to any of aspects 18-22, defined as an LST region that is or exceeds.

Aspect 24. DNA damage agents are cisplatin, carboplatin, oxalaplatin or picoplatin, anthracyclines are epirubincin or doxorubicin, and topoisomerase I inhibitors are campothecin, topotecan or irinotecan, or PARP inhibitors. The method according to any of aspects 18-23, wherein is iniparib, olaparib or velapirib.

Aspect 25. Patients whose test values are not greater than the one or more references in the sample are diagnosed as not likely to respond to the cancer treatment regimen, and (5) (a) respond to the cancer treatment regimen. The steps to recommend, prescribe, initiate, or continue a treatment regimen containing DNA damage agents, anthracyclines, topoisomerase I inhibitors, or PARP inhibitors for patients diagnosed with a high probability of doing so; or (5). (B) Recommend, prescribe, or initiate a treatment regimen that does not contain DNA damage agents, anthracyclines, topoisomerase I inhibitors, or PARP inhibitors for patients diagnosed as unlikely to respond to the cancer treatment regimen. The method of any of aspects 18-24, further comprising any of the steps to be performed or continued.

によって導き出され、かつ、1つまたは複数の参照値が、以下のように、参照集団からの試料におけるインジケーターLOH領域、インジケーターTAI領域およびインジケーターLST領域の数の算術平均を算出すること：

によって導き出される、態様18〜25のいずれかに記載の方法。 Aspect 26. Calculate the arithmetic mean of the number of indicator LOH region, indicator TAI region and indicator LST region in the sample as the test values are as follows:

Calculate the arithmetic mean of the number of indicator LOH region, indicator TAI region and indicator LST region in a sample from a reference group, as derived by and one or more reference values:

The method according to any of aspects 18-25, which is derived from.

Aspect 27. The test value in the sample is at least 2 times, 3 times, 4 times, 5 times, 6 times, 7 times, 8 times, 9 times or 10 times larger than the number of references, or at least 1 standard deviation. 2 standard deviation, 3 standard deviation, 4 standard deviation, 5 standard deviation, 6 standard deviation, 7 standard deviation, 8 standard deviation, 9 standard deviation or 10 standard deviation larger or at least 5%, 10%, 15%, 20 %, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% larger patients, The method of any of aspects 18-26, comprising the step of diagnosing a high likelihood of responding to the cancer treatment regimen.

Aspect 28. A way to treat cancer patients
(1) In a sample containing cancer cells, a step of determining the number of indicator CA regions including indicator LOH region, indicator TAI region and indicator LST region in at least one pair of human chromosomes of the cancer cell of the cancer patient;
(2) The stage of providing a test value derived from the number of the indicator CA regions;
(3) The step of comparing the test value to one or more reference values derived from the number of the indicator CA regions in the reference population; and (4) (a) the reference having at least one test value in the sample. Steps to recommend, prescribe, initiate, or continue a treatment regimen containing DNA inhibitors, anthracyclines, topoisomerase I inhibitors or PARP inhibitors for patients greater than the value; or (4) (b) in that sample At the stage of recommending, prescribing, initiating, or continuing a treatment regimen containing DNA inhibitors, anthracyclines, topoisomerase I inhibitors or PARP inhibitors, for patients whose test value is not greater than at least one of the reference values. Methods, including either.

Aspect 29. 28. The method of aspect 28, wherein at least one pair of human chromosomes represents the entire genome.

Aspect 30. Indicator CA regions are at least 2 pairs, 3 pairs, 4 pairs, 5 pairs, 6 pairs, 7 pairs, 8 pairs, 9 pairs, 10 pairs, 11 pairs, 12 pairs, 13 pairs, 14 pairs, 15 pairs, 16 pairs, 28 or 29, wherein the method of aspect 28 or aspect 29 is determined on 17 pairs, 18 pairs, 19 pairs, 20 pairs or 21 pairs of human chromosomes.

Aspect 31. The method according to any of aspects 28-30, wherein the cancer cells are ovarian cancer cells, breast cancer cells, or esophageal cancer cells.

Aspect 32. The number of references in the indicator LOH area is 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23. , 24, 25, 30, 35, 40, 45, 50 or more, and the number of references in the indicator TAI region is 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 , 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50 or better, and reference to the indicator LST region. Numbers are 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50, or more, the method according to any of aspects 28-31.

Aspect 33. Indicator LOH region has a length of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22 , 23, 24, 25, 30, 35, 40, 45, 50 Megabase or greater, but defined as the LOH region shorter than either the complete chromosome or the complete chromosome arm, the indicator TAI region is longer At least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 , 30, 35, 40, 45, 50 Megabase or greater, but defined as the TAI region that does not extend beyond the centromere, and the indicator LST region is at least 2, 3, 4, 5, in length. 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50 megabase The method according to any of aspects 28-32, defined as an LST region that is or exceeds.

Aspect 34. DNA damage agents are cisplatin, carboplatin, oxalaplatin or picoplatin, anthracyclines are epirubincin or doxorubicin, and topoisomerase I inhibitors are campothecin, topotecan or irinotecan, or PARP inhibitors. 28-33. The method of any of aspects 28-33, wherein is iniparib, olaparib or velapirib.

によって導き出され、かつ、1つまたは複数の参照値が、以下のように、参照集団からの試料におけるインジケーターLOH領域、インジケーターTAI領域およびインジケーターLST領域の数の算術平均を算出すること：

によって導き出される、態様28〜34のいずれかに記載の方法。 Aspect 35. Calculate the arithmetic mean of the number of indicator LOH region, indicator TAI region and indicator LST region in the sample as the test values are as follows:

Calculate the arithmetic mean of the number of indicator LOH region, indicator TAI region and indicator LST region in a sample from a reference group, as derived by and one or more reference values:

The method according to any of aspects 28-34, derived from.

Aspect 36. The test value in the sample is at least 2 times, 3 times, 4 times, 5 times, 6 times, 7 times, 8 times, 9 times or 10 times larger than the number of references, or at least 1 standard deviation. 2 standard deviation, 3 standard deviation, 4 standard deviation, 5 standard deviation, 6 standard deviation, 7 standard deviation, 8 standard deviation, 9 standard deviation or 10 standard deviation larger or at least 5%, 10%, 15%, 20 %, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% larger patients, 28. The method of any of aspects 28-35, comprising the step of diagnosing a high likelihood of responding to the cancer treatment regimen.

Aspect 37. A method for evaluating HRD in cancer cells or their genomic DNA.
(A) In a cancer cell or genomic DNA derived from the cancer cell, a step of detecting an indicator CA region of the cancer cell in at least one pair of human chromosomes, wherein the at least one pair of human chromosomes is a human X / Y sex chromosome pair. Non-steps; and (b) the step of determining the total number of indicator CA regions in at least one pair of human chromosomes,
How to include.

Aspect 38. A method of predicting the status of the BRCA1 and BRCA2 genes in cancer cells.
In cancer cells, the step of determining the total number of indicator CA regions in at least one pair of human chromosomes of said cancer cells; and patients with cancer cells in which the total number is greater than the reference number are likely to be deficient in the BRCA1 or BRCA2 gene. The stage of diagnosing high,
How to include.

Aspect 39. A method of predicting the state of HDR in cancer cells
In cancer cells, the step of determining the total number of indicator CA regions in at least one pair of human chromosomes of said cancer cells; and in cancer cells, patients whose total number is greater than the reference number are diagnosed as having a high likelihood of HDR deficiency. stage,
How to include.

Aspect 40. A method of predicting the response of cancer patients to a cancer treatment regimen that includes DNA damage agents, anthracyclines, topoisomerase I inhibitors, radiation, and / or PARP inhibitors.
In the cancer cells derived from the cancer patient, the step of determining the number of indicator CA regions in at least one pair of human chromosomes of the cancer cells of the cancer patient; The stage of diagnosing a high probability of responding to a treatment regimen,
How to include.

Aspect 41. A method of predicting the response of cancer patients to a treatment regimen
In the cancer cells derived from the cancer patient, the step of determining the total number of indicator CA regions in at least one pair of human chromosomes of the cancer cells of the cancer patient; At the stage of diagnosing a high probability of not responding to a treatment regimen containing docetaxel,
How to include.

Aspect 42. It ’s a way to treat cancer.
(A) The step of determining the total number of indicator CA regions in at least one pair of human chromosomes of cancer cells in cancer cells derived from cancer patients or genomic DNA obtained from them; and (b) said total number of indicator CA regions is referenced. If greater than the number, the cancer patient is given a cancer treatment regimen containing one or more drugs selected from the group consisting of DNA damage agents, anthracyclines, topoisomerase I inhibitors and PARP inhibitors. Stage,
How to include.

Aspect 43. DNA Inhibitors, Anthracyclines, Topoisomerases I for Producing Drugs Useful for Treating Cancer in Patients Identified to Have Cancer Cells Determined to Have a Total of 5 or More Indicator CA Regions Use of one or more drugs selected from the group consisting of inhibitors and PARP inhibitors.

Aspect 44. A system for determining the LOH status of cancer cells in cancer patients.
(A) A sample analyzer configured to generate multiple signals for the genomic DNA of at least one pair of human chromosomes in the cancer cell, and (b) the at least one pair of human chromosomes based on the plurality of signals. Computer subsystem, programmed to calculate the number of indicator CA regions in
System including.

Aspect 45. The computer subsystem compares the number of indicator CA regions to the number of references,
(A) Probability of deletion of BRCA1 gene and / or BRCA2 gene in the cancer cells,
(B) Probability of HDR deficiency in the cancer cells, or (c) Probability of the cancer patient responding to a cancer treatment regimen containing DNA damage agents, anthracyclines, topoisomerase I inhibitors, radiation or PARP inhibitors,
The system according to aspect 8, which is programmed to determine.

Aspect 46. When run on a computer
The step of detecting the presence or absence of any indicator CA region located on one or more of the human chromosomes; and
The step of determining the total number of said indicator CA regions in one or more pairs of chromosomes,
A computer program product embedded in a computer-readable medium.

Aspect 47. At least 500 oligonucleotides capable of hybridizing to multiple polymorphic regions of human genomic DNA; and the computer program product of embodiment 10.
Diagnostic kit, including.

Aspect 48. To determine the total number of indicator CA regions in at least one chromosomal pair of human cancer cells obtained from cancer patients, and (a) the likelihood of deletion of the BRCA1 or BRCA2 gene in the cancer cells,
(B) High likelihood of HDR deficiency in the cancer cells, or (c) the cancer patient responds to a cancer treatment regimen that includes DNA damage agents, anthracyclines, topoisomerase I inhibitors, radiation or PARP inhibitors Probability,
Use of multiple oligonucleotides that can hybridize to multiple polymorphic regions of human genomic DNA to produce diagnostic kits that are useful for detecting.

Aspect 49. Described in any of aspects 37-42, wherein the indicator CA region is the indicator LOH region, the indicator TAI region and the indicator LST region, optionally determined in at least 2, 5, 10 or 21 pairs of human chromosomes. the method of.

Aspect 50. The method according to any of aspects 36-42, wherein the cancer cells are ovarian cancer cells, breast cancer cells, or esophageal cancer cells.

Aspect 51. The method of any of aspects 36-42, wherein the total number of indicator LOH regions, indicator TAI regions, or indicator LST regions is 9, 15, 20 or greater.

Aspect 52. The method of any of aspects 36-42, wherein the indicator LOH region, indicator TAI region or indicator LST region is defined to have a length of about 6, 12 or 15 megabases, or greater.

Aspect 53. The method of any of aspects 36-42, wherein the number of references is 6, 7, 8, 9, 10, 11, 12 or 13 or greater.

Aspect 54. The use according to embodiment 43 or 48, wherein the indicator CA regions are the indicator LOH region, the indicator TAI region and the indicator LST region, optionally determined in at least 2, 5, 10 or 21 pairs of human chromosomes.

Aspect 55. The use according to aspect 43 or 48, wherein the cancer cell is an ovarian cancer cell, a breast cancer cell, or an esophageal cancer cell.

Aspect 56. Use according to aspect 43 or 48, wherein the total number of indicator LOH regions, indicator TAI regions, or indicator LST regions is 9, 15, 20 or greater.

Aspect 57. Use according to aspect 43 or 48, wherein the indicator LOH region, indicator TAI region or indicator LST region is defined to have a length of about 6, 12 or 15 megabases or greater.

Aspect 58. The system according to aspect 44 or 45, wherein the indicator CA regions are the indicator LOH region, the indicator TAI region and the indicator LST region, optionally determined in at least 2, 5, 10 or 21 pairs of human chromosomes.

Aspect 59. 44. The system according to aspect 44 or 45, wherein the cancer cells are ovarian cancer cells, breast cancer cells, or esophageal cancer cells.

Aspect 60. The system according to aspect 44 or 45, wherein the total number of indicator LOH regions, indicator TAI regions, or indicator LST regions is 9, 15, 20 or greater.

Aspect 61. The system according to aspect 44 or 45, wherein the indicator LOH region, indicator TAI region or indicator LST region is defined to have a length of approximately 6, 12 or 15 megabases or greater.

Aspect 62. The computer program product according to embodiment 46, wherein the indicator CA region is the indicator LOH region, the indicator TAI region, and the indicator LST region, optionally determined in at least 2, 5, 10 or 21 pairs of human chromosomes.

Aspect 63. 46. The computer program product according to aspect 46, wherein the cancer cells are ovarian cancer cells, breast cancer cells, or esophageal cancer cells.

Aspect 64. The computer program product according to aspect 46, wherein the total number of indicator LOH regions, indicator TAI regions, or indicator LST regions is 9, 15, 20, or greater.

Aspect 65. A computer program product according to embodiment 46, wherein the indicator LOH region, indicator TAI region, or indicator LST region is defined to have a length of approximately 6, 12 or 15 megabases, or greater.

Aspect 66. The method according to any of aspects 36-42, wherein at least one pair of human chromosomes is not human chromosome 17.

Aspect 67. The use according to aspect 43 or 48, wherein the indicator CA region is not on human chromosome 17.

Aspect 68. The system according to aspect 44 or 45, wherein the indicator CA region is not on human chromosome 17.

Aspect 69. The computer program product according to aspect 46, wherein the indicator CA region is not on human chromosome 17.

Aspect 70. DNA damage agents are cisplatin, carboplatin, oxalaplatin or picoplatin, anthracyclines are epirubincin or doxorubicin, and topoisomerase I inhibitors are campothecin, topotecan or irinotecan, or PARP inhibitors. 40 or 42. The method of aspect 40 or 42, wherein is iniparib, olaparib or velapirib.

Aspect 71. DNA damage agents are platinum-based chemotherapeutic agents, anthracyclines are epirubincin or doxorubicin, topoisomerase I inhibitors are campothecin, topotecan or irinotecan, or PARP inhibitors are iniparib, olaparib or veliparib. (Velapirib), the use according to aspect 48.

Aspect 72. DNA damage agents are platinum-based chemotherapeutic agents, anthracyclines are epirubincin or doxorubicin, topoisomerase I inhibitors are camptothecin, topotecan or irinotecan, or PARP inhibitors are iniparib, olaparib or veliparib. (Velapirib), the system according to aspect 45.

Aspect 73. DNA damage agents are platinum-based chemotherapeutic agents, anthracyclines are epirubincin or doxorubicin, topoisomerase I inhibitors are camptothecin, topotecan or irinotecan, or PARP inhibitors are iniparib, olaparib or beliparib. (Velapirib), the computer program product according to aspect 46.

Aspect 74. (A) In a cancer cell or genomic DNA derived from it, an indicator CA containing at least two types selected from the indicator LOH region, the indicator TAI region, or the indicator LST region in a typical number pair of human chromosomes of the cancer cell. The step of detecting the region; and (b) the step of determining the number and size of the indicator CA region,
How to include.

Aspect 75. The method of aspect 74, wherein a representative number of pairs of human chromosomes represent the entire genome.

Aspect 76. The method of aspect 74, further comprising correlating an increase in the number of indicator CA regions of a particular size with the likelihood of HDR deficiency.

Aspect 77. Specific sizes are about 1.5, 2, 2.5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, The method of aspect 76, wherein it is longer than 30, 35, 40, 45, 50, 75 or 100 megabases and shorter than the length of the entire chromosome containing the indicator CA region.

Aspect 78. The method of aspect 76 or 77, wherein an indicator CA region of a particular size 6, 7, 8, 9, 10, 11, 12 or 13 or larger is correlated with a high likelihood of HDR deficiency.

Aspect 79. A method of determining the prognosis of cancer patients
(A) The indicator LOH region, indicator TAI region, or indicator LST region in at least one pair of human chromosomes of cancer cells of a cancer patient at the stage of determining whether or not a sample containing cancer cells has an HRD signature. The presence of an indicator CA region that exceeds the number of references, including at least two selected from, indicates that the cancer cell has an HRD signature, and (b) (1) the HRD signature is detected in the sample. The stage of diagnosing a patient with a relatively good prognosis, or (b) (2) the stage of diagnosing a patient with no HRD signature detected in the sample, having a relatively poor prognosis
How to include.

Aspect 80. Breast cancer, ovarian cancer, liver cancer, esophageal cancer, lung cancer, head and neck cancer, prostate cancer, colon cancer, rectal cancer, etc. A composition comprising a therapeutic agent selected from the group consisting of DNA damage agents, anthracyclines, topoisomerase I inhibitors and PARP inhibitors for use in the treatment of diseases that are cancers selected from the group consisting of colorectal cancer and pancreatic cancer. Stuff.

Aspect 81. The composition according to embodiment 80, wherein the indicator CA region is determined on at least 2, 5, 10 or 21 pairs of human chromosomes.

Aspect 82. The composition according to embodiment 80, wherein the total number of indicator CA regions is 9, 15, 20 or greater.

Aspect 83. The composition according to embodiment 80, wherein the initial length is about 6, 12 or 15 megabases, or greater.

Aspect 84. The composition according to embodiment 80, wherein the number of references is 6, 7, 8, 9, 10, 11, 12 or 13 or more.

Aspect 85. A way to treat cancer in a patient
The step of determining the number of indicator CA regions in a sample of said patient origin, including at least two types selected from the indicator LOH region, indicator TAI region, or indicator LST region in at least one pair of human chromosomes of cancer cells of a cancer patient. And the stage at which the cancer cell is indicated to have the HRD signature;
The stage of providing test values derived from the number of indicator CA regions;
The test value is combined with one or more reference values (eg, mean, median, trisection, quadrant, quintuple, etc.) derived from the number of indicator CA regions in the reference population. Stage of comparison; and test values are greater than at least one of the above reference values (eg, at least 2x, 3x, 4x, 5x, 6x, 7x, 8x, 9x, or 10x greater. At least 1 standard deviation, 2 standard deviations, 3 standard deviations, 4 standard deviations, 5 standard deviations, 6 standard deviations, 7 standard deviations, 8 standard deviations, 9 standard deviations, or 10 standard deviations larger) Administering an anticancer drug to said patient, or recommending, prescribing, or initiating a treatment regimen containing chemotherapy and / or synthetic lethal agents, at least in part, based on the comparison phase. Or the test value is not greater than at least one of the above reference values (eg, not greater than 2x, 3x, 4x, 5x, 6x, 7x, 8x, 9x or 10x; 1 Standard deviation, 2 standard deviation, 3 standard deviation, 4 standard deviation, 5 standard deviation, 6 standard deviation, 7 standard deviation, 8 standard deviation, 9 standard deviation, or 10 standard deviation not large) The stage of recommending, prescribing, or initiating a treatment regimen free of chemotherapy and / or synthetic lethal agents, at least in part, based on the stage of
How to include.

Aspect 86. 85. The method of aspect 85, wherein the indicator CA region is determined on at least 2, 5, 10 or 21 pairs of human chromosomes.

Aspect 87. The method of aspect 85, wherein the total number of indicator CA regions is 9, 15, 20 or greater.

Aspect 88. The method of aspect 85, wherein the initial length is about 6, 12 or 15 megabases or greater.

Aspect 89. 8. The method of aspect 85, wherein the number of references is 6, 7, 8, 9, 10, 11, 12 or 13 or greater.

Aspect 90. 85. The method of aspect 85, wherein the chemotherapy is selected from the group consisting of DNA damaging agents, anthracyclines and topoisomerase I inhibitors, and / or the synthetic lethality is a PARP inhibitor.

Aspect 91. The DNA damaging agent is cisplatin, carboplatin, oxalaplatin or picoplatin, the anthracycline is epirubincin or doxorubicin, the topoisomerase I inhibitor is camptothecin, topotecan or irinotecan, and / or PARP. 85. The method of aspect 85, wherein the inhibitor is iniparib, olaparib or velapirib.

Aspect 92. A method for evaluating HRD in cancer cells or their genomic DNA.
(A) In cancer cells or genomic DNA derived from them, an indicator CA region containing at least two types selected from an indicator LOH region, an indicator TAI region, or an indicator LST region in at least one pair of human chromosomes of the cancer cell is detected. A step in which the at least one pair of human chromosomes is not a human X / Y sex chromosome pair; and (b) the average number of various indicator CA regions detected in the at least one pair of human chromosomes is calculated. By doing so, the step of determining the average over the total number of indicator CA regions (eg, the arithmetic mean) (eg, if there are 16 indicator LOH regions and 18 indicator LST regions, the arithmetic mean is calculated as 17),
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Aspect 93. A method of predicting the status of the BRCA1 and BRCA2 genes in cancer cells.
In a cancer cell, an average over various total numbers of indicator CA regions, including at least two selected from the indicator LOH region, indicator TAI region, or indicator LST region in at least one pair of human chromosomes of said cancer cell (eg, arithmetic). The step of determining (mean); and the step of correlating the mean over the total number (eg, the arithmetic mean), which is greater than the number of references, with the likelihood of a BRCA1 or BRCA2 gene defect.
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Aspect 94. A method of predicting the state of HDR in cancer cells
In cancer cells, an average across various total numbers of indicator CA regions, including at least two selected from the indicator LOH region, indicator TAI region, or indicator LST region in at least one pair of human chromosomes of said cancer cells (eg, arithmetic). The step of determining the mean; and the step of correlating the mean over the total number (eg, the arithmetic mean), which is greater than the number of references, with the likelihood of HDR deficiency.
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Aspect 95. A method of predicting the response of cancer patients to a cancer treatment regimen that includes DNA damage agents, anthracyclines, topoisomerase I inhibitors, radiation, and / or PARP inhibitors.
In a sample containing cancer cells, an average over various total numbers of indicator CA regions containing at least two selected from the indicator LOH region, indicator TAI region, or indicator LST region in at least one pair of human chromosomes in the sample (eg,). , The stage of determining the arithmetic mean (eg, if there are 16 indicator LOH regions and 18 indicator LST regions, the arithmetic mean is determined to be 17); and the mean over the total number in the sample (eg, arithmetic). A stage in which a patient whose average) is greater than the number of references is determined to be more likely to respond to the cancer treatment regimen.
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Aspect 96. A method of predicting the response of cancer patients to a treatment regimen
In a patient sample containing cancer cells, an average across the total number of indicator CA regions containing at least two selected from the indicator LOH region, indicator TAI region, or indicator LST region in at least one pair of human chromosomes in the patient sample (eg,). , The stage of determining (arithmetic mean); and the stage of diagnosing a patient whose total number of said mean (eg, arithmetic mean) is greater than the reference number in the sample is likely not to respond to a treatment regimen containing paclitaxel or docetaxel.
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Aspect 97. It ’s a way to treat cancer.
(A) In a patient sample containing cancer cells or genomic DNA obtained from them, an indicator containing at least two types selected from the indicator LOH region, indicator TAI region, or indicator LST region in at least one pair of human chromosomes of cancer cells. Steps to determine the mean (eg, arithmetic mean) over various total numbers of CA regions; and (b) DNA inhibitors, anthracyclines, for patients whose total number of indicator CA regions is greater than the reference number in the sample. The stage of administering a cancer treatment regimen containing one or more drugs selected from the group consisting of topoisomerase I inhibitors and PARP inhibitors,
How to include.

Aspect 98. DNA damage agents are cisplatin, carboplatin, oxalaplatin or picoplatin, anthracyclines are epirubincin or doxorubicin, and topoisomerase I inhibitors are campothecin, topotecan or irinotecan, or PARP inhibitors. 95 or 97. The method of aspect 95 or 97, wherein is iniparib, olaparib or velapirib.

Aspect 99. References are averages across various indicator CA regions (eg, arithmetic averages) containing at least two types selected from the indicator LOH region, indicator TAI region, or indicator LST region in at least one pair of human chromosomes of a patient's cancer cells Treatment of diseases that are cancers selected from the group consisting of breast cancer, ovarian cancer, liver cancer, esophageal cancer, lung cancer, head and neck cancer, prostate cancer, colon cancer, rectal cancer, colorectal cancer and pancreatic cancer in larger patients A composition comprising a therapeutic agent selected from the group consisting of DNA damage agents, anthracyclines, topoisomerase I inhibitors and PARP inhibitors for use in.

Aspect 100. A way to treat cancer in a patient
In the patient-derived sample, the average of the total number of indicator CA regions in at least one pair of human chromosomes of cancer cells of a cancer patient (eg, arithmetic mean) is determined and indicated that the cancer cells have an HRD signature. stage;
The step of providing test values derived from an average (eg, arithmetic mean) over various numbers of said indicator CA regions, including at least two selected from the indicator LOH region, indicator TAI region or indicator LST region;
One or more reference values (eg, mean, median, trisection, quaternary) derived from the number of said mean (eg, arithmetic mean) across various indicator CA regions in the reference population. Stages to compare with fractions, quintuples, etc .; and test values are greater than at least one of the above reference values (eg, at least 2x, 3x, 4x, 5x, 6x, 7x). , 8x, 9x, or 10x larger; at least 1 standard deviation, 2 standard deviation, 3 standard deviation, 4 standard deviation, 5 standard deviation, 6 standard deviation, 7 standard deviation, 8 standard deviation, 9 standard deviation, or Based at least in part on the comparison step to reveal that the standard deviation is greater), administer an anticancer drug to the patient, or a treatment regimen that includes chemotherapy and / or a synthetic lethal drug. The stage of recommending, prescribing, or starting; or the test value is not greater than at least one of the above reference values (eg, 2x, 3x, 4x, 5x, 6x, 7x, 8x). Not 9 or 10 times larger; 1 standard deviation, 2 standard deviation, 3 standard deviation, 4 standard deviation, 5 standard deviation, 6 standard deviation, 7 standard deviation, 8 standard deviation, 9 standard deviation, or 10 standard deviation The step of recommending, prescribing, or initiating a therapeutic regimen free of chemotherapy and / or synthetic lethal agents, at least in part, based on the comparative steps that reveal (not significant).
How to include.

Aspect 101. The method of aspect 100, wherein the mean across the various indicator CA regions (eg, the arithmetic mean) is determined on at least 2, 5, 10 or 21 pairs of human chromosomes.

Aspect 102. The method of embodiment 100, wherein the chemotherapy is selected from the group consisting of DNA damaging agents, anthracyclines and topoisomerase I inhibitors, and / or the synthetic lethality is a PARP inhibitor.

Aspect 103. The DNA damaging agent is cisplatin, carboplatin, oxalaplatin or picoplatin, the anthracycline is epirubincin or doxorubicin, the topoisomerase I inhibitor is camptothecin, topotecan or irinotecan, and / or PARP. The method of aspect 100, wherein the inhibitor is iniparib, olaparib or velapirib.

Aspect 104. The method according to aspect 1, wherein the indicator CA region is a combination of an indicator LOH region, an indicator TAI region, and an indicator LST region.

Aspect 105. The method of aspect 104, wherein the number of references is 42.

Aspect 106. 9. The method of aspect 9, wherein the indicator CA region is a combination of the indicator LOH region, the indicator TAI region, and the indicator LST region.

Aspect 107. The method of aspect 106, wherein the number of references is 42.

Aspect 108. 18. The method of aspect 18, wherein the indicator CA region is a combination of an indicator LOH region, an indicator TAI region, and an indicator LST region.

Aspect 109. The method of aspect 108, wherein the number of references is 42.

Aspect 110. 28. The method of aspect 28, wherein the number of references is 42.

Aspect 111. 33. The method of aspect 37, wherein the indicator CA region is a combination of the indicator LOH region, the indicator TAI region, and the indicator LST region.

Aspect 112. 11. The method of aspect 111, wherein the number of references is 42.

Aspect 113. 38. The method of aspect 38, wherein the indicator CA region is a combination of the indicator LOH region, the indicator TAI region, and the indicator LST region.

Aspect 114. The method of aspect 113, wherein the number of references is 42.

Aspect 115. 39. The method of aspect 39, wherein the indicator CA region is a combination of the indicator LOH region, the indicator TAI region, and the indicator LST region.

Aspect 116. The method of aspect 115, wherein the number of references is 42.

Aspect 117. The method of aspect 40, wherein the indicator CA region is a combination of the indicator LOH region, the indicator TAI region, and the indicator LST region.

Aspect 118. The method of aspect 117, wherein the number of references is 42.

Aspect 119. 41. The method of aspect 41, wherein the indicator CA region is a combination of the indicator LOH region, the indicator TAI region, and the indicator LST region.

Aspect 120. 119. The method of aspect 119, wherein the number of references is 42.

Aspect 121. 42. The method of aspect 42, wherein the indicator CA region is a combination of the indicator LOH region, the indicator TAI region, and the indicator LST region.

Aspect 122. 12. The method of aspect 121, wherein the number of references is 42.

Aspect 123. 7. The method of aspect 79, wherein the indicator CA region is a combination of the indicator LOH region, the indicator TAI region, and the indicator LST region.

Aspect 124. The method of aspect 123, wherein the number of references is 42.

Aspect 125. 85. The method of aspect 85, wherein the indicator CA region is a combination of the indicator LOH region, the indicator TAI region, and the indicator LST region.

Aspect 126. The method of aspect 125, wherein the number of references is 42.

Aspect 127. An in vitro method that predicts patient response to a cancer treatment regimen that includes DNA damage agents, anthracyclines, topoisomerase I inhibitors, or PARP inhibitors.
(1) In a sample containing cancer cells, a step of determining the number of indicator CA regions including the indicator LOH region, the indicator TAI region, and the indicator LST region in at least one pair of human chromosomes of the cancer cells of the cancer patient;
(2) Steps of combining the indicator CA regions to obtain test values as follows: test value = (number of indicator LOH regions) + (number of indicator TAI regions) + (number of indicator LST regions); and ( 3) The stage of providing a reference value for comparison with the test value,
How to include.

Aspect 128. 12. The method of aspect 127, wherein the reference value corresponds to the 5th percentile value of the indicator CA region score in the training cohort of patients with HDR deficiency.

Aspect 129. The method of aspect 127 or aspect 128, wherein the reference value is 42.

Aspect 130. The method according to any of aspects 127-129, further comprising the step of comparing the test value with the reference value.

Aspect 131. The method of any of aspects 127-130, further comprising diagnosing a patient whose test value exceeds a reference value in a sample as likely to respond to a cancer treatment regimen.

Aspect 132. The decision stages are at least 2 pairs, at least 3 pairs, at least 4 pairs, at least 5 pairs, at least 6 pairs, at least 7 pairs, at least 8 pairs, at least 9 pairs, at least 10 pairs, at least 11 pairs, at least 12 pairs, at least. At least 150, 200, 250 in 13 pairs, at least 14 pairs, at least 15 pairs, at least 16 pairs, at least 17 pairs, at least 18 pairs, at least 19 pairs, at least 20 pairs, at least 21 pairs, or at least 22 pairs of autosomal chromosomes. , 300, 350, 400, 450, 500, 600, 700, 800, 900, 1,000, 1,500, 2,000, 2,500, 3,000, 3,500, 4,000, 4,500, 5,000, 6,000, 7,000, 8,000, 9,000, 10,000, 11,000, 12,000 , 13,000, 14,000, 15,000, 16,000, 17,000, 18,000, 19,000, 20,000, 25,000, 30,000, 35,000, 40,000, 45,000, 50,000, 60,000, 70,000 80,000, 90,000, 100,000, 125,000, 150,000, 175,000, 200,000, 250,000, 300,000, Any of aspects 127-131, including the step of assaying a sample to measure the copy number of each allele for 400,000, 500,000, 600,000, 700,000, 800,000, 900,000, 1,000,000 or more polymorphic genomic loci. The method described in.

Aspect 133. 13. The method of aspect 132, wherein the determination step comprises assaying polymorphic genomic loci in at least 10 pairs of autosomal chromosomes.

Aspect 134. 13. The method of aspect 133, in an autosomal chromosome with 22 pairs of polymorphic genomic loci.

Aspect 135. The method according to any of aspects 132-134, wherein the determination step comprises assaying a sample to measure the copy number of each allele for at least 5,000 polymorphic genomic loci in an autosomal pair.

Aspect 136. 13. The method of aspect 135, wherein the determination step comprises assaying a sample to measure the copy number of each allele for at least 10,000 polymorphic genomic loci in an autosomal pair.

Aspect 137. 136. The method of aspect 136, wherein the determination step comprises assaying a sample to measure the copy number of each allele for at least 50,000 polymorphic genomic loci in an autosomal pair.

The present invention will be further described in the following examples, but these do not limit the scope of the invention described in the claims.

Example 1-LOH and TAI region scores across breast cancer subtypes, and association with BRCA1 / 2 deficiency
LOH signatures based on whole-genome tumor LOH profiles have been developed that are highly correlated with defects in other HDR pathway genes in BRCA1 / 2 and ovarian cancer (Abkevich, et al., Patterns of Genomic Loss of Heterozygosity Predict Homologous Recombination). Repair Defects, BR. J. CANCER (2012)), which predicts the response to DNA-damaging agent (eg, platinum-based neoadjuvant) therapy in cancer (Telli et al., Homologous Recombination Deficiency (HRD) score predicts response following neoadjuvant. platinum-based therapy in triple-negative and BRCA1 / 2 mutation-associated breast cancer (BC), CANCER RES. (2012)). A second score based on TAI also shows a strong correlation with BRCA1 / 2 deficiency and predicts response to platinum-based drug treatment in triple-negative breast cancer (Birkbak et al., Telomeric allelic imbalance indicates defective DNA repair and sensitivity to DNA). -damaging agents, CANCER DISCOV. (2012)). In this study, we examined the frequency of BRCA1 / 2 deficiency and increased LOH or TAI region scores across breast cancer subtypes defined by ER / PR / HER2 status.

Frozen tumors were purchased from three commercial tissue biobanks. Approximately 50 randomly identified tumors from each of the four breast cancer subtypes (triple negative, ER + / HER2-, ER- / HER2 +, ER + / HER2 +) were selected for analysis. We have developed a targeted custom hybridization panel that targets BRCA1, BRCA2 and 50,000 selected SNPs across the entire genome. This panel was used in combination with sequencing on the Illumina HiSeq 2500 to analyze tumors for BRCA1 / 2 somatic and germline mutations, including extensive rearrangements, as well as SNP allelic levels. Methylation of the BRCA1 promoter was determined by qPCR assay (SA Biosciences). When available, DNA from normal tissues was used to determine whether the detrimental mutation was germline or somatic.

（表３）突然変異スクリーニングを、17件のBRCA1／2突然変異体からの対応する正常組織に対して行った。17例の個体のうち13例（76.5％）が生殖細胞系突然変異を有した。

^* 各個体はBRCA1において1つの生殖細胞系突然変異および1つの体細胞突然変異を有した。

（表４）：LOHスコアまたはTAIスコアとBRCA1／2欠損との関連

SNP data were analyzed using an algorithm that determines the most probable allele-specific copy count at each SNP position. The LOH region score was calculated by calculating the number of LOH regions that are longer than 15 Mb but shorter than the length of the entire chromosome. The TAI region score was calculated by calculating the number of telomere regions with allelic imbalances that are longer than 11 Mb but do not exceed the centromere. Samples with poor quality SNP data and / or high levels of normal DNA contamination were excluded. Robust scores were obtained from 191 of the 213 samples.

(Table 2) BRCA1 / 2 deficiency in breast cancer IHC subtype

(Table 3) Mutation screening was performed on the corresponding normal tissues from 17 BRCA1 / 2 mutants. Of the 17 individuals, 13 (76.5%) had germline mutations.

^* Each individual had one germline mutation and one somatic mutation in BRCA1.

(Table 4): Relationship between LOH score or TAI score and BRCA1 / 2 deficiency

FIG. 5 shows the LOH region score and the TAI region score by IHC subtype of breast cancer. 5A: LOH score; 5B: TAI score. Blue bar: BRCA1 / 2 deficient sample. Red bar: BRCA1 / 2 intact sample. FIG. 6 shows the correlation between the LOH region score and the TAI region score (correlation coefficient = 0.69). X-axis: LOH score; Y-axis: TAI score; Red dot: Intact sample; Blue dot: BRCA1 / 2 deficient sample. The area under the dot is proportional to the number of samples with a combination of LOH score and TAI score (p = 10 ^-39 ).

Logistic regression analysis was used to predict BRCA1 / 2 deficiency based on LOH and TAI scores. Both scores were significant in multivariate analysis (chi-squared for LOH was 10.8 and for TAI was 44.7; p = 0.001 and 2.3 ^* 10 ^-11 ). The best model for differentiating BRCA1 / 2-deficient samples from intact samples is the 0.32 ^* LOH region score + 0.68 ^* TAI region score (p = 9 ^* 10 ^-18 ).

CONCLUSIONS: Increased LOH and TAI region scores are highly associated with BRCA1 / 2 deficiency in all subtypes of breast cancer, respectively; LOH and TAI region scores are highly correlated; complex The CA region score (ie, the combination of LOH and TAI) shows the optimal correlation with BRCA1 / 2 deficiency in this dataset. Based on this disclosure, the combination of LOH-HRD and TAI-HRD scores can predict the response to DNA-damaging agents and other agents (eg, platinum-based drug therapy) in triple-negative breast cancer, and other breast cancers. Allows extended use of platinum-based agents for subtypes.

Example 2-Association of LOH region score, TAI region score and LST region score across breast cancer subtypes, and BRCA1 / 2 deficiency As described in Example 1, the ratio of SNP allele frequencies was determined to obtain the LOH region score. , TAI region score and LST region score were used for calculation. The LST score was defined as the number of discontinuities between regions longer than 10 megabases with stable copy numbers after screening out regions shorter than 3 megabases. We have observed that the LST score increases with ploidy in both intact and defective samples. Therefore, in this Example 2, instead of using a ploidy-specific cutoff, we modified the LST region score by adjusting it by ploidy: LSTm = LST-kP, in the equation, P is ploidy and k is a constant. According to multivariate logistic regression analysis using defects as outcomes and LST and P as predictors, k = 15.5.

Of the 214 samples, 191 scored to pass the QC criteria used. Thirty-eight of these samples were BRCA1 / 2 deficient. The corresponding p-values from the Kolmogorov-Smirnov test for LOH region scores are 8 ^* 10 ^{-12 , 2 *} 10 ^-16 for TAI region scores, and 8 ^* 10 ^-8 for LST region scores. Of the 191 samples, 53 had triple-negative breast cancer, including 22 with BRCA1 / 2 deficiency. ^{The corresponding p-values were 6 *} 10 ^-6 , 3 ^* 10 ^-6 and 0.0002 for the LOH region score, TAI region score and LST region score, respectively. When the same analysis is performed for each of the individual breast cancer subtypes, a significant p-value is found for at least one score for all subtypes (Table 5). The distribution of scores is shown in FIGS. 7A-C for comparison between BRCA1 / 2 deficient samples and BRCA1 / 2 intact samples.

The scores were then analyzed to determine if they were correlated (Figures 2D-F). The correlation coefficient between the LOH region score and the TAI region score is 0.69 (p = 10 ^-39 ), between LOH and LST is 0.55 (p = 2 ^* 10 ^-19 ), and between TAI and LST. The interval was 0.39 (p = 10 ^-9 ).

Logistic regression analysis was used to predict BRCA1 / 2 deficiency based on LOH region score, TAI region score and LST region score. All three scores were significant in multivariate analysis (chi-squared for LOH was 5.1 (p = 0.02), TAI was 44.7 (p = 2 ^* 10 ^-11 ), and LST was. 5.4 (p = 0.02)). The best model for differentiating BRCA1 / 2 deficient and intact samples in this dataset was 0.21 ^* LOH + 0.67 ^* TAI + 0.12 ^* LST (p = 10 ^-18 ). This Example 2 extends the conclusions of Example 1 (ie, a model that combines the LOH region score and the TAI region score) to a model that combines the LOH region score, the TAI region score, and the LST region score.

Other clinical data available for many of the samples included stage, grade and age at diagnosis. Stage information was available in 64 of 191 samples. The correlation coefficient between the stage and the LOH region score (0.07) and TAI region score (0.1) was not significant. Grade information was available in 164 of 191 samples. The correlation coefficient between grade and LOH region score (0.33) and TAI region score (0.23) is significant (p = 2 ^* 10 ^-5 and 0.004, respectively). Age at diagnosis was found in 184 of 191 samples. The correlation coefficient (-0.13) between age and LOH region score was not significant. The correlation coefficient (-0.25) between age and TAI region score was significant (p = 0.0009).

(Table 5)

Example 3-Arithmetic Mean of LOH Region Scores, TAI Region Scores and LST Region Scores Across Breast Cancer Subtypes, and Association with BRCA1 / 2 Deficiency The following studies have HRD scores as described herein. It shows how the efficacy of drugs targeting BRCA1 / 2 deficiency and HR deficiency in triple-negative breast cancer (TNBC) can be predicted. Breast tumor samples were assayed for BRCA1 / 2 mutations and promoter methylation to determine the rate of BRCA1 / 2 deficiency across breast cancer subtypes. The three HRD scores described in Example 2 were determined for the samples and then the association with BRCA1 / 2 deficiency was examined using the arithmetic mean of the LOH / TAI / LST scores. Analysis of the neoadjuvant TNBC cohort treated with cisplatin was further performed on the relationship between all three HRD scores and response.

Invasive breast tumor samples and corresponding normal tissues were obtained from three vendors. Samples were selected so that approximately equal numbers were obtained for all breast cancer subtypes defined by IHC analysis for ER, PR and HER2. BRCA1 promoter methylation analysis was performed by qPCR. BRCA1 / 2 mutation screening and genome-wide SNP profiles were generated using custom-made Agilent SureSelect XT capture followed by sequencing with Illumina HiSeq 2500. Using these data, HRD-LOH score, HRD-TAI score and HRD-LST score were calculated.

SNP microarray and clinical data were downloaded from the public repository for the Cisplatin-1 and Cisplatin-2 clinical trial cohorts. No BRCA1 / 2 mutation data were available for one of these cohorts. All three HRD scores were calculated from public data and analyzed for association with response to cisplatin. The two cohorts were combined for increased power.

To calculate the HRD score, SNP data was analyzed using an algorithm to determine the most probable allele-specific copy number at each SNP position. HRD-LOH was calculated by calculating the number of LOH regions that were longer than 15 Mb but shorter than the length of the entire chromosome. The HRD-TAI score was calculated by calculating the number of regions with allelic imbalances that were longer than 11 Mb and spread to one of the subtelomeres but did not exceed the centromere. The HRD-LST score was defined as the number of discontinuities between regions longer than 10 Mb after sifting through regions shorter than 3 Mb.

The composite score was the arithmetic mean of the LOH / TAI / LST scores. All p-values were taken from a logistic regression model with a dependent variable of response to BRCA deficiency or cisplatin.

^* BRCA1のインタクトな機能的コピーを依然として保つ個体1例を含む。
† BRCA1に関する機能的状態を判定できなかった個体1例を含む。 Table 6 shows the BRCA1 / 2 mutation and BRCA1 promoter methylation frequencies across the four breast cancer subtypes. BRCA1 / 2 mutant analysis was successful on 100% of the samples, but large-scale rearrangement analysis was less robust, with 198 of 214 samples passing QC criteria. Met. Adverse mutations were observed in 24 of 214 individuals (1 with somatic mutations in BRCA1 and germline mutations in BRCA2). Corresponding normal DNA was available in 23 of the 24 mutants, which were used to determine whether the identified mutations were germline or somatic. BRCA1 promoter methylation analysis was successfully performed on 100% of the samples. FIG. 9 illustrates the HRD score in BRCA1 / 2 deficient samples.

(Table 6)

^* Includes one individual who still retains an intact functional copy of BRCA1.
† Includes 1 individual whose functional status with respect to BRCA1 could not be determined.

Table 7 shows the association between the three HRD scores in the breast cohort of all participants and BRCA1 / 2 deficiency. The composite score was the arithmetic mean of the three HRD scores.

(Table 7)

Table 8 shows the association between HRD scores and pCR (Miller-Payne 5) in TNBC treated with cisplatin in the neoadjuvant setting. Data are from the Cisplatin-1 study (Silver et al., Efficacy of neoadjuvant Cisplatin in triple-negative breast cancer. J. CLIN. ONCOL. 28: 1145-53 (2010)) and the Cisplatin-2 study (Birkbak et al, (Birkbak et al,). It was available from the sample from 2012)). pCR was defined as a patient with Miller-Payne 5 status after neoadjuvant therapy. The HRD-composite was the arithmetic mean of the three HRD scores.

(Table 8)

CONCLUSIONS: BRCA1 / 2 deficiency and increased HRD score were observed in all breast cancer subtypes, and HRD score detected BRCA1 / 2 deficiency. All three HRD scores predicted / detected a therapeutic response to cisplatin in TNBC. Meaning of the three HRD scores (arithmetic mean) detected BRCA1 / 2 status in the breast cohort of all participants and cisplatin response in the second independent TNBC cohort. Arithmetic mean HRD-complexes were stronger predictors / detectors of BRCA1 / 2 deficiency or therapeutic response than individual HRD scores.

Example 4-BRCA1 / 2 state multivariate analysis and DNA-based assay for homologous recombination defects Previous examples have described DNA-based scores for measuring homologous recombination defects (HRD). , Each score has been demonstrated to be significantly associated with BRCA1 / 2 deficiency, as is the HRD-composite score, which is defined as the arithmetic mean of the three HRD scores. In this example, (1) the association between each of the three scores and the HRD-composite score, (2) the association between the clinical variable and the HRD-composite score, and (3) the clinical variable and the HRD-composite score. The results of previous examples are extended by examining the association between and BRCA1 / 2 deficiency.

METHODS: The analysis in Example 4 includes the same 197 patient samples as described in previous examples. Briefly, 215 breast tumor samples were purchased as fresh frozen specimens from three vendors. Samples were selected to give approximately the same number of representative breast cancer subtypes by IHC analysis for ER, PR and HER2. 198 samples yielded reliable HRD scores according to the Kolmogorov-Smirnov quality standard. One patient who passed the HRD score was excluded from the analysis because it had an unusual breast cancer subtype (ER / PR + HER2-). Details of the patient's tumor and clinical characteristics are shown in Table 9.

Patient clinical data were provided for 91 variables, but data for most variables were scarce to include in the analysis. Breast cancer subtypes (TNBC, ER + / HER2-, ER- / HER2 +, ER + / HER2 +) were available for all patients. Other variables considered were age at diagnosis (obtained in 196 of 197 patients), stage (obtained in 191 of 197 patients) and grade (obtained in 190 of 197 patients). Was).

(Table 9)

BRCA1 / 2 mutation screening and genome-wide SNP profiles were generated using custom-made Agilent SureSelect XT capture followed by sequencing with Illumina HiSeq 2500. Methylation of the BRCA-1 promoter region was determined by qPCR. Samples with greater than 10% methylation were classified as methylated.

The HRD score is the three HRD scores combined in the "HRD-composite score" discussed in Example 4, heterozygoous loss (LOH) profile (HRD-LOH) of whole-genome tumors, telomere allelic imbalance. Calculated from (HRD-TAI) and large-scale state transition (HRD-LST).

BRCA1 / 2 deficiency was defined as loss of function due to mutations in BRCA1 or BRCA2 or methylation of the promoter region of BRCA1 with heterozygosity loss (LOH) in the affected gene.

All statistical analyzes were performed using R version 3.0.2. All reported p-values are bilateral. Statistical tools used include Spearman rank test correlation, Kruskal-Wallis one-way ANOVA, and logistic regression.

For logistic regression modeling, the HRD score and age at diagnosis were encoded as numerical variables. Breast cancer stage and subtype were encoded as categorical variables. The grade was coded as both a numerical variable and a categorical variable, but unless otherwise specified, it was a categorical variable. Encoding grades as numerical variables means that when comparing grade 2 and grade 1 patients, and when comparing grade 3 patients to grade 2 patients, the odds increase for BRCA1 / 2 deficiency is the same. Inappropriate except.

The p-values reported for univariate logistic regression models are based on partial likelihood ratios. The multivariate p-value includes all predictors, except for the complete model (including all applicable predictors) and the reduced model (the evaluated predictors and all interaction terms involving the evaluated predictors). ) Based on the partial likelihood ratio for changes in deviation. Odds ratios for HRD scores are reported for the interquartile range.

Results: The pairwise correlation between HRD-LOH score, HRD-TAI score and HRD-LST score was examined graphically (Fig. 1) and quantified by Spearman rank test correlation. The Spearman rank test correlation is preferred over the more commonly used Pearson product-moment correlation because the HRD score distribution has a right tail and outliers were observed. All pairwise comparisons of the scores showed a positive correlation with 0 (p <10 ^-16 ).

The degree of independent BRCA1 / 2 deficiency information captured by each of the HRD-LOH, HRD-TAI, and HRD-LST scores used all three scores as predictors of BRCA1 / 2 deficiency. Measured by examining a multivariate logistic regression model (Table 10). The HRD-TAI score captured significant BRCA1 / 2 deficiency information independent of that obtained by the other two scores (p = 0.00016), as did the HRD-LST score (p = 0.00014). ). At the 5% significance level, the HRD-LOH score did not add significantly independent BRCA1 / 2 deficiency information (p = 0.069).

(Table 10)

Table 10 illustrates the results of a ternary multivariate logistic regression model using HRD-LOH, HRD-TAI and HRD-LST as predictors of BRCA1 / 2 deficiency.

To assess whether the HRD-composite score adequately captures BRCA1 / 2 deficiency information for its three components, we examined three bivariate logistic regression models. Each model included an HRD-composite score and one of the HRD-LOH score, HRD-TAI score or HRD-LST score. None of the component scores made a significant addition to the HRD-composite score at the 5% significance level (HRD-LOH p = 0.89, HRD-TAI p = 0.090, HRD-LST p = 0.28). This suggests that the HRD-composite score adequately captured BRCA1 / 2 deficiency information in the HRD-LOH score, HRD TAI score and HRD-LST score.

Finally, the HRD-composite score was also compared with a model-based composite score optimized to predict BRCA1 / 2 deficiency in this patient set. The HRD-composite score weights the HRD-LOH score, HRD-TAI score, and HRD-LST score equally, while the model-based score is approximately the HRD-LOH score or HRD-LST score relative to the HRD-TAI score. Double the weight. The formula for model-based scores is
HRD-model = 0.11 x (HRD-LOH) + 0.25 x (HRD-TAI) + 0.12 x (HRD-LST)
Given by.

Univariate analysis results (Table 11) show that HRD-model scores outperform HRD-composite scores by approximately single digits (HRD model p = 2.5 × 10 ^-25 , HRD-composite p). = 1.1 x 10 ^-24 ).

(Table 11)

Table 11 shows the results of univariate logistic regression. The odds ratio for the HRD score is reported per IQR of the score. The odds ratio for age is reported per year. The odds ratio for grade (numerical value) is per unit.

In the bivariate logistic regression model, the HRD-model score did not add significant independent BRCA1 / 2 deficiency information to the HRD-composite score (p = 0.089). This further suggests that the HRD-composite score adequately captures BRCA1 / 2 deficiency information in the HRD-LOH score, HRD-TAI score and HRD-LST score.

The relationship between clinical variables and HRD-composite scores is shown in Figure 12. The HRD-composite score was significantly correlated with tumor grade (Spearman correlation 0.23, p = 0.0017). The correlation with breast cancer stage and age at diagnosis was 0 at the 5% level, which was not significantly different. According to the Kruskal-Wallis one-way ANOVA, the mean HRD-composite score was significantly different for each breast cancer subtype (p = 1.6 × 10 ^-5 ).

The heterogeneity of HRD-composite scores between clinical subpopulations was examined by examining the significance of the interaction terms in a multivariate logistic regression model. For each clinical variable, we added a section on HRD-composite score interactions for models that included all clinical variables and HRD-composite scores. None of the interaction terms reached significance at the 5% significance level. Therefore, there is no evidence that the probability of BRCA1 / 2 deficiency conferred by the HRD-composite score varies between clinical subpopulations.

Similar tests for HRD-LOH score, HRD-TAI score and HRD-LST score respectively show significant interactions between HRD-TAI score and age (p = 0.0072) and grade (p = 0.015), as well as Significant interactions between HRD-LST scores and breast cancer subtypes were indicated (p = 0.021). In the adjustment for multiple comparisons, only the interaction between HRD-TAI score and age remained significant at the 5% level (p = 0.029). The significance of this interaction suggests that the increased probability of BRCA1 / 2 deficiency per unit increase in HRD-TAI score decreases with increasing age.

The relationship between clinical variables and BRCA1 / 2 deficiency is presented in Figure 13. Clinical variables and HRD-composite scores were evaluated in univariate (Table 11) and multivariate (Table 12) logistic regression models. Odds ratios for HRD scores are reported per IQR. Odds ratios for age at diagnosis are reported annually.

(Table 12)

Table 12 shows the results of multivariate logistic regression. The odds ratio for the HRD score is reported per IQR of the score. The odds ratio for age is reported per year.

In univariate analysis, each of the HRD scores (HRD-LOH, HRD-TAI, HRD-LST, HRD-composite and HRD-model) was significantly associated with BRCA1 / 2 deficiency. It was pointed out that the higher the score, the higher the probability of loss. There was a significant association that the older the age at diagnosis, the lower the risk of BRCA1 / 2 deficiency (p = 0.0071). Univariate results (both categorical and numerical) for breast cancer subtypes and tumor grades were also statistically significant. Cancer stage was not associated with BRCA1 / 2 status.

In multivariate analysis, we examined models based on HRD-composite scores and all available clinical variables. The HRD-composite score captured significant BRCA1 / 2 deficiency information that was not captured by clinical variables (p = 1.2 × 10 ^-16 ). Of the available clinical variables, only age at diagnosis remained significant in a multivariate environment (p = 0.027). When the grade was encoded as a categorical variable, it was not statistically significant (p = 0.40). The grade was also not significant when encoded as a numerical variable (p = 0.28). Secondary and tertiary effects on HRD-composite scores were tested in a multivariate model that included all clinical variables, but were not statistically significant.

Consideration. In this Example 4, the frequency of BRCA1 / 2 deficiency across the four subtypes of breast cancer defined by the IHC subtype classification ranged from approximately 9% to approximately 16%. Sequencing of matched tumor and normal DNA samples suggested that approximately 75% of the observed mutations were of germline origin. Although the main method for loss of the second allele in breast cancer is via LOH, nearly 24% of tumors subsequently also carry somatic deleterious mutations in the second allele. In addition, sporadic breast tumors were found in one individual carrying a deleterious somatic mutation in BRCA2.

All three HRD scores showed a strong correlation with BRCA1 / 2 deficiency regardless of subtype, and due to the frequency of score increase, a significant proportion of all breast tumor subtypes were defective in the homologous recombination DNA repair pathway. It was suggested to possess. Considering these findings, especially in combination with Example 3 above, agents that target or utilize DNA damage repair (eg, platinum-based anticancer agents) are tumors from all subtypes of breast cancer. May be effective through a subset of (those with homologous recombination deficiencies as detected by the present disclosure).

In the clinical setting, these HRD scores, either alone or in combination, are best captured using an assay compatible with formalin-fixed, paraffin-embedded core needle biopsy samples (“FFPE”). is there. Only very low quantities and low quality DNA can be obtained with this type of sample. DNA extracted from these FFPE-treated samples often does not perform well with SNP microarray analysis.

Target enrichment techniques based on liquid hybridization have been developed to create libraries for next-generation sequencing. These methods allow targeted sequencing of regions of interest after reduced genomic complexity, resulting in reduced sequencing costs. Preliminary studies have indicated that the available assays are compatible with DNA derived from FFPE DNA. In this Example 4, we report the development of a capture panel targeting approximately 54,000 SNPs distributed throughout the genome. The number of alleles from the sequencing information obtained by this panel can be used for copy counts and LOH reconstructions, as well as for the calculation of all three HRD scores. In addition, BRCA1 and BRCA2 capture probes may be included in the panel as in Example 4, which allows for quality mutation screening for deleterious mutants in these genes in the same assay. ..

All three scores are significantly correlated with each other, suggesting that they all measure the same core genomic phenomenon. However, logistic regression analysis suggests that the combination of scores can result in a stronger association with BRCA1 / 2 deficiency in this dataset.

Double-stranded DNA damage by combining a robust score capable of identifying tumors with a defect in homologous recombination DNA repair with assay compatibility with formalin-fixed, paraffin-embedded clinical pathological specimens. It facilitates diagnostic identification and classification of patients who are likely to respond to drugs that target repair. In addition, such agents may be useful across all subtypes of breast cancer in which HRD is detected according to the present disclosure.

Example 5-High HRD Threshold (eg, an example of an HRD signature)
In this example, the determination of high HRD is articulated. Threshold references were chosen to have high sensitivity for detecting HRD in breast and ovarian tumors that were nonspecific to both therapeutic response and outcome. The total number of LOH region, TAI region and LST region was determined. To calculate the HRD score, SNP data was analyzed using an algorithm to determine the most probable allele-specific copy count at each SNP position. HRD-LOH was calculated by calculating the number of LOH regions that were longer than 15 Mb but shorter than the length of the entire chromosome. The HRD-TAI score was calculated by calculating the number of regions with allelic imbalances that were longer than 11 Mb and spread to one of the subtelomeres but did not exceed the centromere. The HRD-LST score was defined as the number of discontinuities between regions longer than 10 Mb after sifting through regions shorter than 3 Mb. The combined score (HRD score) was the sum of the LOH / TAI / LST scores.

The training set was collected from four different cohorts (497 breasts and 561 ovaries). This set consisted of 78 breast tumors and 190 ovarian tumors lacking a functional copy of BRCA1 or BRCA2, which means that the distribution of HRD scores in BRCA-deficient samples corresponds to the distribution of scores across HRD samples. To do. The 5th percentile value of the HRD score in the training set was set as the threshold, which gives a sensitivity of more than 95% for the detection of HR deficiency. High HRD (or HRD signature) was defined as having a reference score of 42 or higher (Figure 14).

Example 6-HRD Predicts Response to Cisplatin in Triple Negative Breast Cancer In this example, the HRD scores described herein are effective for agents targeting HR deficiency in triple negative breast cancer (TNBC) samples. Demonstrate how sex can be predicted. Analysis of the neoadjuvant TNBC cohort treated with cisplatin was examined against the relationship between all three HRD scores and response. All p-values were taken from a logistic regression model with the response to cisplatin as the dependent variable.

Of the 70 samples from the cisplatin cohort (70 individual patients), 62 were assessed for HR deficiency (the tumors possessed by 8 were inadequate for analysis). Of these, 31 (50%) were HR deficient, 22 (35%) were non-HR deficient, and 9 (15%) were unconfirmed. Figure 15 presents a histogram showing the distribution of HRD scores in the cohort. Scores of 42 and above were considered to have high HRD (see also Example 5). The bimodality illustrated in FIG. 15 indicates that the HRD score effectively distinguished between HR-deficient and non-deficient conditions in tumors. A complete pathological response (pCR) associated with long-term survival was defined as a residual cancer level (RBC) of 0, which was observed in 11 of 59 (19%) samples. Pathological response (PR) was defined as an RBC of 0 or 1, which was observed in 22 of 59 (37%) samples. These overall response rates were correlated with the expected value of monotherapy.

Statistical analysis was performed according to the default Statistical Analysis Plan (SAP), which includes a primary analysis, a secondary analysis, and a BRCA wild-type subset analysis.

（表１３）反応を予測するためにHR欠損を用いた一次分析 In the primary analysis, HR-deficient states were used to predict reactions in 50 samples. As shown in Table 13, HR-deficient samples provided better predictors of response for both PR and pCR. For example, 52% of HR-deficient samples had a pathological response, whereas non-deficient samples had a pathological response of 9.5%. Similarly, 28% of HR-deficient samples had a complete pathological response, whereas non-deficient samples had a pathological response of 0%.

(Table 13) Primary analysis using HR deficiency to predict response

（表１４）反応を予測するために定量的HRDスコアを用いた二次分析 In the secondary analysis, the quantitative HRD scores described in Example 5 were used to predict reactions in 48 samples. As shown in Table 14, HRD scores were significantly higher in responder-derived samples than in non-responders, either defined as PR or pCR.

(Table 14) Secondary analysis using quantitative HRD scores to predict response

（表１５）病理学的奏効の多変数モデル
* IQR当たりのオッズ比 The distribution of HRD scores within each response class for secondary analysis, defined by the state of the BRCA mutation, is illustrated in Figure 16, where the dotted line at position 42 is between the low and high scores. Represents the HRD threshold. Figure 17 shows the reaction curve for the secondary analysis, or the probability of PR associated with each value of the quantitative HRD score. The curve shown in Figure 17 was modeled by four parameters: the shape and scale of the curve, as well as generalized logistic regression to estimate the lower and upper bounds. The darkly painted boxes contrast the probability of reaction in HR-deficient and non-HR-deficient samples. Table 15 shows that HR status was still significantly associated with pathological response in the secondary analysis.

(Table 15) Multivariable model of pathological response
* Odds ratio per IQR

（表１６）定量的HRD構成要素スコアとPRの対比 The contrast between the individual HRD component scores and the pathological response is shown in Table 16 and in Figure 18. Table 16 shows that the response was predicted by each component score, ie LOH, TAI and LST, and their sum, ie HRD score, was equally significant or more significant than any of the individual components. It shows that (HRD p-value = 3.1 × 10 ^-4 ). FIG. 18 illustrates a strong pairwise correlation between component scores.

(Table 16) Comparison of quantitative HRD component score and PR

（表１７）反応を予測するためにBRCA突然変異状態を用いた二次分析 The secondary analysis also examined the association between BRCA1 / 2 mutation status and response. Table 17 confirms that BRCA mutations are associated with a response; however, this association is not significant in this cohort (n = 51), and BRCA mutations are not as predictable as HR deficiency. There wasn't.

(Table 17) Secondary analysis using BRCA mutations to predict response

（表１８）BRCA野生型試料における反応を予測するためにHR欠損を用いたサブセット分析 To demonstrate that HR deficiency is predictable in samples without BRCA1 / 2 mutations, a further subset analysis was performed using HR deficiency status in 38 BRCA wild-type samples. As shown in Table 18, HR-deficient samples provided better response predictors for both PR and pCR in BRCA wild-type samples. For example, 52.6% of HR-deficient samples had a pathological response, whereas 10.5% of non-deficient samples had a pathological response. Similarly, 26.3% of HR-deficient samples had a complete pathological response, whereas 0% of non-deficient samples had a complete pathological response.

(Table 18) Subset analysis using HR deficiency to predict reaction in BRCA wild-type samples

（表１９）BRCA野生型試料における反応を予測するために定量的HRDスコアを用いたサブセット分析 Subset analysis using quantitative HRD scores was further performed on 38 BRCA wild-type samples. As shown in Table 19, samples with high HRD (scores of 42 and above) provided better response predictors for both PR and pCR in BRCA wild-type samples.

(Table 19) Subset analysis using quantitative HRD scores to predict response in BRCA wild-type samples

In conclusion, this example demonstrates that the sum of all three HRD scores significantly predicted a response to cisplatin treatment in TNBC.

Other Aspects Although the present invention has been described with its detailed description, the above description is intended to illustrate the invention and is not intended to be limiting, which may be defined by the appended claims. Need to be understood. Other aspects, advantages and changes are within the scope of the following claims.

Claims (33)

An in vitro method that predicts a patient's response to a cancer treatment regimen, including DNA damage agents, anthracyclines, topoisomerase I inhibitors, or PARP inhibitors.
(1) A step of determining the number of indicator LOH region, indicator TAI region, and indicator CA region including indicator LST region in at least one pair of human chromosomes of cancer cells of a cancer patient in a sample containing breast cancer cells.
here,
(A) The indicator LOH region is a LOH region longer than the 15 megabase, but shorter than the overall length of each chromosome in which the LOH region is located.
The indicator TAI region is (i) a TAI region with an allelic imbalance that extends to one of the subtelomeres, (ii) does not cross the centromere, and (iii) is 11 megabases or longer.
(C) The indicator LST region is the discontinuity of somatic copy counts along the length of the chromosome that exists between two regions with a length of at least 10 megabases after sifting off regions shorter than 3 megabases. And (2) indicate that the patient is likely to respond to the cancer treatment regimen if the sum of the indicator LOH region, indicator TAI region, and indicator LST region in the sample is greater than the number of references. A method that includes the steps to be performed. The method of claim 1, wherein at least one pair of human chromosomes represents the entire genome. Indicator CA regions are at least 2 pairs, 3 pairs, 4 pairs, 5 pairs, 6 pairs, 7 pairs, 8 pairs, 9 pairs, 10 pairs, 11 pairs, 12 pairs, 13 pairs, 14 pairs, 15 pairs, 16 pairs, The method of claim 1 or 2, as determined on 17 pairs, 18 pairs, 19 pairs, 20 pairs or 21 pairs of human chromosomes. The number of references includes a combination of the number of references in the indicator LOH area, the number of references in the indicator TAI area, and the number of references in the indicator LST area, and the number of references in the indicator LOH area is 2, 3, 4, 5, 6, 7, 8 , 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50 or Above, the number of references in the indicator TAI area is 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22 , 23, 24, 25, 30, 35, 40, 45, 50 or more, and the number of references in the indicator LST region is 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 40 45, 50 or more, claims 1 to The method described in any one of 3. The method according to any one of claims 1 to 4, wherein the number of references is 32. DNA damage agents are cisplatin, carboplatin, oxaliplatin or picoplatin, anthracyclines are epirubicin or doxorubicin, topotecanase I inhibitors are camptothecin, topotecan or irinotecan, or PARP inhibitors are iniparib, olaparib or beliparib, The method according to any one of claims 1 to 5. It further includes steps in which the patient is shown to be likely to recommend, prescribe, initiate, or continue the cancer treatment regimen if it is shown to be likely to respond to the cancer treatment regimen. , The method according to any one of claims 1 to 6. An in vitro method that predicts patient response to a cancer treatment regimen that includes a platinum agent.
(1) A step of determining the number of indicator LOH region, indicator TAI region, and indicator CA region including indicator LST region in at least one pair of human chromosomes of cancer cells of a cancer patient in a sample containing breast cancer cells.
here,
(A) The indicator LOH region is a LOH region longer than the 15 megabase, but shorter than the overall length of each chromosome in which the LOH region is located.
The indicator TAI region is (i) a TAI region with an allelic imbalance that extends to one of the subtelomeres, (ii) does not cross the centromere, and (iii) is 11 megabases or longer.
(C) The indicator LST region is the discontinuity of somatic copy counts along the length of the chromosome that exists between two regions with a length of at least 10 megabases after sifting off regions shorter than 3 megabases. Is;
(2) The step of determining whether a sample containing cancer cells from the patient is deficient in BRCA1 or BRCA2; and (3) in that sample, (a) indicator LOH region, indicator TAI region, and indicator LST. If the total number of regions is greater than the number of references, or (b) BRCA1 or BRCA2 is deficient, or both (a) and (b), the patient has the cancer treatment regimen. A method that includes steps that are shown to be more likely to respond to. The method of claim 8, wherein at least one pair of human chromosomes represents the entire genome. Indicator CA regions are at least 2 pairs, 3 pairs, 4 pairs, 5 pairs, 6 pairs, 7 pairs, 8 pairs, 9 pairs, 10 pairs, 11 pairs, 12 pairs, 13 pairs, 14 pairs, 15 pairs, 16 pairs, The method of claim 8 or 9, as determined on 17 pairs, 18 pairs, 19 pairs, 20 pairs or 21 pairs of human chromosomes. The number of references includes a combination of the number of references in the indicator LOH area, the number of references in the indicator TAI area, and the number of references in the indicator LST area, and the number of references in the indicator LOH area is 2, 3, 4, 5, 6, 7, 8 , 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50 or Above, the number of references in the indicator TAI area is 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22 , 23, 24, 25, 30, 35, 40, 45, 50 or more, and the number of references in the indicator LST region is 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50 or more, claim 8 The method according to any one of ~ 10. The method according to any one of claims 8 to 11, wherein the number of references is 32. Platinum-based anticancer agent is cisplatin, carboplatin, oxaliplatin (oxalaplatin) or picoplatin method of any one of claims 8-12. Any one of claims 8-13, wherein the sample is deficient in BRCA1 or BRCA2 if a mutation, heterozygosity loss or high methylation that is harmful to either BRCA1 or BRCA2 is detected in the sample. Item description method. Methylation is at least 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, or 50% of the analyzed BRCA1 or BRCA2 promoter CpG, or better. 14. The method of claim 14, wherein highly methylation is detected when detected. An in vitro method that predicts patient response to a cancer treatment regimen that includes DNA damage agents, anthracyclines, topoisomerase I inhibitors, or PARP inhibitors.
(1) A step of determining the number of indicator LOH region, indicator TAI region, and indicator CA region including indicator LST region in at least one pair of human chromosomes of cancer cells of a cancer patient in a sample containing breast cancer cells.
here,
(A) The indicator LOH region is a LOH region longer than the 15 megabase, but shorter than the overall length of each chromosome in which the LOH region is located.
The indicator TAI region is (i) a TAI region with an allelic imbalance that extends to one of the subtelomeres, (ii) does not cross the centromere, and (iii) is 11 megabases or longer.
(C) The indicator LST region is the discontinuity of somatic copy counts along the length of the chromosome that exists between two regions with a length of at least 10 megabases after sifting off regions shorter than 3 megabases. Is;
(2) The stage of providing a test value derived from the number of the indicator CA regions;
(3) The step of comparing the test value to one or more reference values derived from the number of the indicator CA regions in the reference group; and (4) the test value is the one or more references in the sample. A method comprising a step in which the patient is indicated to be more likely to respond to the cancer treatment regimen if greater than the value. 16. The method of claim 16, wherein at least one pair of human chromosomes represents the entire genome. Indicator CA regions are at least 2 pairs, 3 pairs, 4 pairs, 5 pairs, 6 pairs, 7 pairs, 8 pairs, 9 pairs, 10 pairs, 11 pairs, 12 pairs, 13 pairs, 14 pairs, 15 pairs, 16 pairs, 16. The method of claim 16 or 17, as determined on 17 pairs, 18 pairs, 19 pairs, 20 pairs or 21 pairs of human chromosomes. The number of indicator LOH regions in the reference group is 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22 , 23, 24, 25, 30, 35, 40, 45, 50 or more, and the number of indicator TAI regions in the reference group is 2, 3, 4, 5, 6, 7, 8, 9, 10 , 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50 or better, and reference The number of indicator LST regions in the population is 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50, or more, the method of any one of claims 16-18. The method according to any one of claims 16 to 19, wherein the reference value is 32. DNA damage agents are cisplatin, carboplatin, oxalaplatin or picoplatin, anthracyclines are epirubincin or doxorubicin, and topoisomerase I inhibitors are campothecin, topotecan or irinotecan, or PARP inhibitors. The method of any one of claims 16-20, wherein is iniparib, olaparib or velapirib. A stage in which the patient is not likely to respond to the cancer treatment regimen if the test value is not greater than the one or more references in the sample, and (5) (a) the patient. Recommends and prescribes a treatment regimen containing DNA damage agents, anthracyclines, topoisomerase I inhibitors, or PARP inhibitors to patients if they are shown to be more likely to respond to the cancer treatment regimen. , Stages that are likely to begin or continue; or (5) (b) DNA damage to the patient if the patient is shown to be unlikely to respond to the cancer treatment regimen. Claim 16 to further include any step of recommending, prescribing, initiating, or indicating the potential for continuation of a treatment regimen that is free of agents, anthracyclines, topoisomerase I inhibitors, or PARP inhibitors. The method according to any one of 21. Calculate the arithmetic mean of the number of indicator LOH region, indicator TAI region and indicator LST region in the sample as the test values are as follows:

Calculate the arithmetic mean of the number of indicator LOH region, indicator TAI region and indicator LST region in a sample from a reference group, as derived by and one or more reference values:

The method of any one of claims 16-22, which is derived from. The test value in the sample is at least 2 times, 3 times, 4 times, 5 times, 6 times, 7 times, 8 times, 9 times or 10 times larger than one or more reference values, or at least 1 standard deviation, 2 standard deviation, 3 standard deviation, 4 standard deviation, 5 standard deviation, 6 standard deviation, 7 standard deviation, 8 standard deviation, 9 standard deviation or 10 standard deviation larger or at least 5%, 10%, 15%, 20 %, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% The method of any one of claims 16-23, comprising a step in which the patient is shown to be more likely to respond to the cancer treatment regimen. A method of predicting the likelihood that a cancer patient will be treated with a treatment regimen that includes DNA damage agents, anthracyclines, topoisomerase I inhibitors or PARP inhibitors.
(1) In a sample containing breast cancer cells, a step of determining the number of indicator CA regions including indicator LOH region, indicator TAI region and indicator LST region in at least one pair of human chromosomes of the cancer cell of the cancer patient.
here,
(A) The indicator LOH region is a LOH region longer than the 15 megabase, but shorter than the overall length of each chromosome in which the LOH region is located.
The indicator TAI region is (i) a TAI region with an allelic imbalance that extends to one of the subtelomeres, (ii) does not cross the centromere, and (iii) is 11 megabases or longer.
(C) The indicator LST region is the discontinuity of somatic copy counts along the length of the chromosome that exists between two regions with a length of at least 10 megabases after sifting off regions shorter than 3 megabases. Is;
(2) The stage of providing a test value derived from the number of the indicator CA regions;
(3) The step of comparing the test value to one or more reference values derived from the number of the indicator CA regions in the reference population; and (4) (a) the reference having at least one test value in the sample. Steps indicating that the patient may be recommended, prescribed, initiated, or continued with a therapeutic regimen containing DNA damage agents, anthracyclines, topoisomerase I inhibitors or PARP inhibitors if greater than the value. Or (4) (b) the patient is free of DNA damage agents, anthracyclines, topoisomerase I inhibitors or PARP inhibitors if the test value is not greater than at least one of the reference values in the sample. A method that includes either recommending, prescribing, initiating, or indicating the likelihood of continuing a treatment regimen. 25. The method of claim 25, wherein at least one pair of human chromosomes represents the entire genome. Indicator CA regions are at least 2 pairs, 3 pairs, 4 pairs, 5 pairs, 6 pairs, 7 pairs, 8 pairs, 9 pairs, 10 pairs, 11 pairs, 12 pairs, 13 pairs, 14 pairs, 15 pairs, 16 pairs, 25 or 26. The method of claim 25 or 26, as determined on 17 pairs, 18 pairs, 19 pairs, 20 pairs or 21 pairs of human chromosomes. The number of indicator LOH regions in the reference group is 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22 , 23, 24, 25, 30, 35, 40, 45, 50 or more, and the number of indicator TAI regions in the reference group is 2, 3, 4, 5, 6, 7, 8, 9, 10 , 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50 or better, and reference The number of indicator LST regions in the population is 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50, or more, the method of any one of claims 25-27. The method according to any one of claims 25 to 28, wherein the number of references is 32. DNA damage agents are cisplatin, carboplatin, oxalaplatin or picoplatin, anthracyclines are epirubincin or doxorubicin, and topoisomerase I inhibitors are campothecin, topotecan or irinotecan, or PARP inhibitors. 25. The method of any one of claims 25-29, wherein is iniparib, olaparib or velapirib. Calculate the arithmetic mean of the number of indicator LOH region, indicator TAI region and indicator LST region in the sample as the test values are as follows:

Calculate the arithmetic mean of the number of indicator LOH region, indicator TAI region and indicator LST region in a sample from a reference group, as derived by and one or more reference values:

The method of any one of claims 25-30, which is derived from. The test value in the sample is at least 2 times, 3 times, 4 times, 5 times, 6 times, 7 times, 8 times, 9 times or 10 times larger than one or more reference values, or at least 1 standard deviation, 2 standard deviation, 3 standard deviation, 4 standard deviation, 5 standard deviation, 6 standard deviation, 7 standard deviation, 8 standard deviation, 9 standard deviation or 10 standard deviation larger or at least 5%, 10%, 15%, 20 %, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% The method of any one of claims 25-31, comprising the stage in which the patient is indicated to be more likely to be treated by the cancer treatment regimen. The test values are as follows:
Test value = (number of indicator LOH regions) + (number of indicator TAI regions) + (number of indicator LST regions)
The method of any one of claims 16-22 and 25-30, as determined as.

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